atomiuk commented 6 years ago

Hi, when calling VEP with the dbNSFP plugin as follows

/data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep \ --species homo_sapiens \ --input_file test.vcf \ --output_file ouput.txt \ --dir_cache /data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep_data/ \ --offline \ --tab \ --assembly GRCh37 \ --fasta /data2/NGS/pipeline_data_GATK/b37/human_g1k_v37_decoy.fasta \ --force_overwrite \ --plugin dbNSFP,dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

I get the error message Use of uninitialized value in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 197. Use of uninitialized value in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 197.

Two columns named aaref and genename are added to the output, but their content is always "-".

For generating the dbNSFPv3.5a file for GRCh37 is used the following commands:

unzip dbNSFPv3.5a.zip head -n1 dbNSFP3.5a_variant.chr1 > h cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz tabix -s 8 -b 9 -e 9 dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz

I tested some of the variants with tabix, e.g. tabix dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz 1:3703503-3703502 and got the expected output.

I used the following VCF as input:

fileformat=VCFv4.2 | | | | | | | | |

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GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output somatic_mutect2_w_interval_filtered.vcf.gz --contamination-table 62419341_matched_calculatecontamination.table --variant somatic_mutect2_w_interval.vcf.gz --log-somatic-prior -6.0 --tumor-lod 5.3 --normal-artifact-lod 0.0 --normal-p-value-threshold 0.001 --max-germline-posterior 0.1 --max-alt-allele-count 1 --min-pcr-slippage-size 8 --pcr-slippage-rate 0.1 --pcr-slippage-p-value 0.001 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 5 --max-events-in-region 2 --max-strand-artifact-probability 0.99 --min-strand-artifact-allele-fraction 0.01 --max-contamination-probability 0.1 --unique-alt-read-count 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.7.0,Date="August 13, 2018 7:23:01 AM CEST">

GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample 62419341_S1 --normal-sample 62432268_S85 --panel-of-normals /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/PON/PON_centogene_5samples_wo_interval.vcf.gz --germline-resource /data2/NGS/pipeline_data_GATK/b37/af-only-gnomad.raw.sites.b37.vcf.gz --af-of-alleles-not-in-resource 2.5E-6 --bam-output somatic_mutect2_w_interval.bam --output somatic_mutect2_w_interval.vcf.gz --intervals /data2/NGS/SURESELECT/SureSelect_Human_All_Exon_V6_r2/S07604514_Padded_wo_chr.bed --input /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/piped/62419341_recal.bam --input /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/piped/62432268_recal.bam --reference /data2/NGS/pipeline_data_GATK/b37/human_g1k_v37_decoy.fasta --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter --genotype-pon-sites false --genotype-germline-sites false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --max-mnp-distance 1 --ignore-itr-artifacts false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20 --max-read-length 2147483647 --min-read-length 30 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.7.0,Date="August 10, 2018 8:14:24 PM CEST">

INFO= | | |

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INFO= | |

INFO= |

INFO= | | | | |

Mutect Version=2.1 | | | | | | | | |

contig= | | | | | | | |

filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS. |

normal_sample=62432268_S85 | | | | | | | |

source=FilterMutectCalls | | | | | | | | |

source=Mutect2 | | | | | | | | |

tumor_sample=62419341_S1 | | | | | | | |

CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | 62419341_S1 | 62432268_S85

1 | 2288813 | . | A | C | . | PASS | DP=54;ECNT=2;NLOD=4.82;N_ART_LOD=-1.326e+00;POP_AF=1.231e-04;P_CONTAM=7.950e-09;P_GERMLINE=-2.546e+00;TLOD=9.59 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB | 0/1:7,4:0.444:3,3:4,1:30,23:166,219:60:6:0|1:2288807_A_C:0.00,0.364,0.364:0.026,0.025,0.949 | 0/0:16,0:0.204:6,0:10,0:36,0:207,0:0:0:0|1:2288807_A_C 1 | 3319365 | . | G | A | . | PASS | DP=211;ECNT=1;NLOD=27.99;N_ART_LOD=-1.975e+00;POP_AF=2.462e-05;P_CONTAM=6.191e-11;P_GERMLINE=-5.000e+01;TLOD=10.12 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:110,7:0.065:57,5:53,2:25,32:172,144:60:14:0.040,0.061,0.060:8.086e-03,0.011,0.981 | 0/0:93,0:5.448e-03:44,0:49,0:35,0:202,0:0:0 1 | 3703502 | . | G | A | . | PASS | DP=228;ECNT=1;NLOD=27.69;N_ART_LOD=-1.984e+00;POP_AF=2.461e-05;P_CONTAM=0.00;P_GERMLINE=-2.649e+01;TLOD=188.90 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:47,63:0.559:23,37:24,26:26,33:164,156:60:16:0.545,0.556,0.573:0.022,0.018,0.960 | 0/0:92,0:0.040:55,0:37,0:35,0:194,0:0:0 1 | 6196558 | . | C | A | . | PASS | DP=40;ECNT=1;NLOD=5.12;N_ART_LOD=-1.255e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-4.891e+00;TLOD=46.65 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:8,15:0.656:6,7:2,8:35,34:243,202:60:12:0.00,0.657,0.652:0.030,0.025,0.946 | 0/0:17,0:6.261e-05:12,0:5,0:39,0:236,0:0:0 1 | 16892365 | . | C | G | . | PASS | DP=135;ECNT=1;NLOD=16.25;N_ART_LOD=-1.744e+00;POP_AF=2.500e-06;P_CONTAM=7.325e-11;P_GERMLINE=-2.981e+01;TLOD=9.52 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:72,6:0.090:46,3:26,3:36,38:228,252:34:15:0.071,0.020,0.077:1.394e-04,0.945,0.055 | 0/0:54,0:9.392e-03:33,0:21,0:39,0:259,0:0:0 1 | 23768482 | . | G | T | . | PASS | DP=68;ECNT=1;NLOD=9.29;N_ART_LOD=-1.521e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-9.531e+00;TLOD=78.37 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:11,23:0.676:5,15:6,8:31,34:261,213:60:10:0.636,0.667,0.676:0.029,0.022,0.948 | 0/0:31,0:0.047:17,0:14,0:42,0:270,0:0:0 1 | 28834054 | . | C | G | . | PASS | DP=76;ECNT=1;NLOD=5.42;N_ART_LOD=-1.279e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-5.263e+00;TLOD=74.78 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:35,23:0.400:19,17:16,6:31,36:185,171:60:15:0.394,0.354,0.397:0.031,0.020,0.949 | 0/0:18,0:4.370e-05:11,0:7,0:40,0:193,0:0:0 1 | 35885282 | . | G | A | . | PASS | DP=108;ECNT=1;NLOD=11.39;N_ART_LOD=-1.622e+00;POP_AF=2.500e-06;P_CONTAM=2.604e-04;P_GERMLINE=-2.310e+01;TLOD=5.54 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:56,3:0.083:21,1:35,2:36,35:169,181:60:9:0.051,0.00,0.051:0.011,0.012,0.977 | 0/0:38,0:0.080:14,0:24,0:39,0:254,0:0:0 1 | 45810775 | . | G | A | . | PASS | DP=473;ECNT=1;NLOD=44.55;N_ART_LOD=-2.174e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-6.374e+01;TLOD=210.83 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:241,75:0.246:127,39:114,36:26,34:180,168:60:13:0.212,0.232,0.237:0.022,5.412e-03,0.972 | 0/0:148,0:3.455e-03:67,0:81,0:37,0:217,0:0:0 1 | 46495103 | . | A | G | . | PASS | DP=131;ECNT=1;NLOD=13.55;N_ART_LOD=-1.663e+00;POP_AF=2.461e-05;P_CONTAM=0.00;P_GERMLINE=-2.020e+01;TLOD=28.06 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:66,13:0.194:32,9:34,4:34,30:160,164:60:20:0.131,0.152,0.165:0.016,0.012,0.972 | 0/0:45,0:6.126e-05:16,0:29,0:40,0:218,0:0:0 1 | 46876343 | . | C | T | . | PASS | DP=47;ECNT=1;NLOD=7.83;N_ART_LOD=-1.431e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-7.646e+00;TLOD=39.46 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:7,14:0.657:4,7:3,7:36,31:209,228:60:23:0.00,0.667,0.667:0.063,0.016,0.921 | 0/0:26,0:7.222e-05:12,0:14,0:39,0:312,0:0:0 1 | 59247747 | . | T | C | . | PASS | DP=150;ECNT=1;NLOD=13.80;N_ART_LOD=-1.671e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.310e+01;TLOD=167.75 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:52,52:0.500:25,24:27,28:34,36:169,174:60:20:0.475,0.485,0.500:0.017,0.021,0.962 | 0/0:46,0:2.244e-03:23,0:23,0:38,0:221,0:0:0 1 | 64624767 | . | C | T | . | PASS | DP=101;ECNT=1;NLOD=10.84;N_ART_LOD=-1.568e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.709e+01;TLOD=24.19 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:53,10:0.181:30,6:23,4:25,33:173,165:60:13:0.141,0.131,0.159:9.859e-03,0.021,0.969 | 0/0:36,0:1.220e-04:15,0:21,0:36,0:223,0:0:0 1 | 77883147 | . | G | C | . | PASS | DP=16;ECNT=1;NLOD=2.41;N_ART_LOD=-9.542e-01;POP_AF=2.500e-06;P_CONTAM=1.136e-04;P_GERMLINE=-2.168e+00;TLOD=6.15 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:6,2:0.250:2,1:4,1:31,38:223,307:60:18:0.00,0.253,0.250:0.023,0.025,0.952 | 0/0:8,0:2.356e-05:6,0:2,0:42,0:287,0:0:0 1 | 79355581 | . | A | T | . | PASS | DP=38;ECNT=1;NLOD=4.52;N_ART_LOD=-1.204e+00;POP_AF=2.500e-06;P_CONTAM=8.891e-15;P_GERMLINE=-5.011e+00;TLOD=16.90 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:17,6:0.265:8,2:9,4:33,34:193,134:60:21:0.263,0.00,0.261:0.019,0.031,0.951 | 0/0:15,0:6.311e-05:5,0:10,0:39,0:268,0:0:0 1 | 89521878 | . | T | C | . | PASS | DP=83;ECNT=1;NLOD=9.28;N_ART_LOD=-1.504e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.002e+01;TLOD=41.01 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:34,16:0.327:18,3:16,13:32,31:195,203:50:28:0.313,0.273,0.320:0.033,0.018,0.950 | 0/0:31,0:3.354e-03:15,0:16,0:36,0:222,0:0:0 1 | 100671860 | . | AT | A | . | PASS | DP=80;ECNT=1;NLOD=5.71;N_ART_LOD=-1.379e+00;POP_AF=0.012;P_CONTAM=4.575e-07;P_GERMLINE=-4.280e+00;RPA=6,5;RU=T;STR;TLOD=5.95 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:27,5:0.287:12,1:15,4:25,32:217,188:60:20:0.152,0.111,0.156:0.014,0.022,0.964 | 0/0:19,0:0.174:4,0:15,0:36,0:226,0:0:0 1 | 110735165 | . | G | A | . | PASS | DP=215;ECNT=1;NLOD=17.46;N_ART_LOD=-1.777e+00;POP_AF=2.462e-05;P_CONTAM=0.00;P_GERMLINE=-1.650e+01;TLOD=181.04 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:82,60:0.433:40,33:42,27:26,33:172,168:60:13:0.384,0.414,0.423:0.023,0.015,0.962 | 0/0:58,0:0.017:29,0:29,0:34,0:191,0:0:0 1 | 115604725 | . | A | C | . | PASS | DP=27;ECNT=2;NLOD=4.81;N_ART_LOD=-1.230e+00;POP_AF=3.692e-04;P_CONTAM=3.966e-05;P_GERMLINE=-2.455e+00;TLOD=9.75 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB | 0/1:8,3:0.273:8,2:0,1:32,30:165,262:60:13:0|1:115604725_A_C:0.00,0.273,0.273:0.032,0.019,0.949 | 0/0:16,0:8.319e-04:11,0:5,0:35,0:177,0:0:0:0|1:115604725_A_C 1 | 118488548 | . | A | G | . | PASS | DP=36;ECNT=1;NLOD=3.91;N_ART_LOD=-1.146e+00;POP_AF=2.500e-06;P_CONTAM=5.738e-06;P_GERMLINE=-6.267e+00;TLOD=6.10 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:20,3:0.131:12,1:8,2:32,31:209,152:60:28:0.00,0.131,0.130:0.024,0.015,0.961 | 0/0:13,0:5.911e-05:8,0:5,0:38,0:223,0:0:0 1 | 120471809 | . | C | A | . | PASS | DP=252;ECNT=1;NLOD=31.77;N_ART_LOD=-2.030e+00;POP_AF=2.500e-06;P_CONTAM=3.204e-11;P_GERMLINE=-6.195e+01;TLOD=13.16 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:136,7:0.056:64,4:72,3:32,34:173,145:60:20:0.040,0.040,0.049:8.985e-03,4.997e-03,0.986 | 0/0:106,0:7.595e-03:47,0:59,0:40,0:217,0:0:0 1 | 120612340 | . | C | G | . | PASS | DP=106;ECNT=2;NLOD=9.33;N_ART_LOD=-1.517e+00;POP_AF=2.709e-04;P_CONTAM=1.336e-06;P_GERMLINE=-2.036e+01;TLOD=11.08 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:67,5:0.079:39,3:28,2:30,36:246,236:40:24:0.071,0.00,0.069:0.025,0.010,0.964 | 0/0:31,0:0.030:10,0:21,0:42,0:243,0:0:0 1 | 145017837 | . | CTTCCTTCCTT | C | . | PASS | DP=44;ECNT=2;NLOD=3.01;N_ART_LOD=-1.041e+00;POP_AF=1.240e-04;P_CONTAM=8.572e-12;P_GERMLINE=-3.970e+00;TLOD=19.33 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB | 0/1:28,6:0.176:16,3:12,3:37,32:181,122:60:11:0|1:145017837_CTTCCTTCCTT_C:0.172,0.00,0.176:7.833e-05,0.983,0.017 | 0/0:10,0:3.162e-05:4,0:6,0:39,0:214,0:0:0:0|1:145017837_CTTCCTTCCTT_C 1 | 151810924 | . | G | A | . | PASS | DP=305;ECNT=1;NLOD=25.44;N_ART_LOD=-1.932e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-5.923e+01;TLOD=34.27 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:185,18:0.110:97,14:88,4:26,33:181,156:60:14:0.020,0.091,0.089:0.490,1.062e-03,0.509 | 0/0:87,1:0.033:42,0:45,1:35,11:256,567:60:35 1 | 156639990 | . | C | T | . | PASS | DP=233;ECNT=1;NLOD=15.65;N_ART_LOD=-1.766e+00;POP_AF=2.500e-06;P_CONTAM=1.124e-15;P_GERMLINE=-4.392e+01;TLOD=18.73 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:140,9:0.115:81,4:59,5:32,34:174,201:60:25:0.061,0.040,0.060:3.221e-03,0.026,0.970 | 0/0:52,0:0.100:28,0:24,0:40,0:224,0:0:0 1 | 158613108 | . | T | C | . | PASS | DP=80;ECNT=1;NLOD=8.98;N_ART_LOD=-1.502e+00;POP_AF=2.500e-06;P_CONTAM=2.464e-07;P_GERMLINE=-1.559e+01;TLOD=6.21 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:40,4:0.125:19,4:21,0:34,25:185,192:60:27:0.081,0.040,0.091:6.133e-03,0.045,0.948 | 0/0:30,0:0.034:17,0:13,0:39,0:239,0:0:0 1 | 160106522 | . | AA | TT | . | PASS | DP=383;ECNT=1;NLOD=55.38;N_ART_LOD=-2.279e+00;POP_AF=2.500e-06;P_CONTAM=3.582e-04;P_GERMLINE=-1.026e+02;TLOD=7.01 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:183,4:0.023:93,0:90,4:34,34:185,141:60:19:0.020,0.020,0.021:6.809e-03,2.756e-03,0.990 | 0/0:184,0:0.031:103,0:81,0:37,0:212,0:0:0 1 | 161009918 | . | C | T | . | PASS | DP=96;ECNT=1;NLOD=7.53;N_ART_LOD=-1.422e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.331e+01;TLOD=29.79 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:57,13:0.187:30,7:27,6:32,31:211,232:60:13:0.162,0.162,0.186:0.053,7.608e-03,0.939 | 0/0:25,0:0.019:12,0:13,0:43,0:252,0:0:0 1 | 165738001 | . | TC | AA | . | PASS | DP=214;ECNT=1;NLOD=17.46;N_ART_LOD=-1.774e+00;POP_AF=2.500e-06;P_CONTAM=6.150e-11;P_GERMLINE=-5.103e+01;TLOD=16.97 | GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB | 0/1:148,7:0.045:76,4:72,3:31,33:175,170:60:7:0.030,0.040,0.045:0.015,3.328e-03,0.981 | 0/0:58,0:8.482e-03:30,0:28,0:37,0:216,0:0:0

Thanks in advance for your help!

Best, Stefan

aparton commented 6 years ago

Hi Stefan,

Could you please update your dbNSFP.pm file to the latest version and try again? We updated dbNSFP recently, and that should hopefully fix your issue.

Kind Regards, Andrew

On 24 Aug 2018, at 10:22, atomiuk notifications@github.com wrote:

Hi, when calling VEP with the dbNSFP plugin as follows

/data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep --species homo_sapiens --input_file test.vcf --output_file ouput.txt --dir_cache /data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep_data/ --offline --tab --assembly GRCh37 --fasta /data2/NGS/pipeline_data_GATK/b37/human_g1k_v37_decoy.fasta --force_overwrite --plugin dbNSFP,dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

I get the error message Use of uninitialized value in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 197. Use of uninitialized value in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 197.

Two columns named aaref and genename are added to the output, but their content is always "-".

For generating the dbNSFPv3.5a file for GRCh37 is used the following commands:

unzip dbNSFPv3.5a.zip head -n1 dbNSFP3.5a_variant.chr1 > h cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz tabix -s 8 -b 9 -e 9 dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz

I tested some of the variants with tabix, e.g. tabix dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz 1:3703503-3703502 and got the expected output.

I used the following VCF as input:

fileformat=VCFv4.2

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GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output somatic_mutect2_w_interval_filtered.vcf.gz --contamination-table 62419341_matched_calculatecontamination.table --variant somatic_mutect2_w_interval.vcf.gz --log-somatic-prior -6.0 --tumor-lod 5.3 --normal-artifact-lod 0.0 --normal-p-value-threshold 0.001 --max-germline-posterior 0.1 --max-alt-allele-count 1 --min-pcr-slippage-size 8 --pcr-slippage-rate 0.1 --pcr-slippage-p-value 0.001 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 5 --max-events-in-region 2 --max-strand-artifact-probability 0.99 --min-strand-artifact-allele-fraction 0.01 --max-contamination-probability 0.1 --unique-alt-read-count 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.7.0,Date="August 13, 2018 7:23:01 AM CEST">

GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample 62419341_S1 --normal-sample 62432268_S85 --panel-of-normals /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/PON/PON_centogene_5samples_wo_interval.vcf.gz --germline-resource /data2/NGS/pipeline_data_GATK/b37/af-only-gnomad.raw.sites.b37.vcf.gz --af-of-alleles-not-in-resource 2.5E-6 --bam-output somatic_mutect2_w_interval.bam --output somatic_mutect2_w_interval.vcf.gz --intervals /data2/NGS/SURESELECT/SureSelect_Human_All_Exon_V6_r2/S07604514_Padded_wo_chr.bed --input /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/piped/62419341_recal.bam --input /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/piped/62432268_recal.bam --reference /data2/NGS/pipeline_data_GATK/b37/human_g1k_v37_decoy.fasta --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter --genotype-pon-sites false --genotype-germline-sites false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --max-mnp-distance 1 --ignore-itr-artifacts false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20 --max-read-length 2147483647 --min-read-length 30 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.7.0,Date="August 10, 2018 8:14:24 PM CEST">

INFO=

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Mutect Version=2.1

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filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.

normal_sample=62432268_S85

source=FilterMutectCalls

source=Mutect2

tumor_sample=62419341_S1

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 62419341_S1

1 2288813 . A C . PASS 1 3319365 . G A . PASS 1 3703502 . G A . PASS 1 6196558 . C A . PASS 1 16892365 . C G . PASS 1 23768482 . G T . PASS 1 28834054 . C G . PASS 1 35885282 . G A . PASS 1 45810775 . G A . PASS 1 46495103 . A G . PASS 1 46876343 . C T . PASS 1 59247747 . T C . PASS 1 64624767 . C T . PASS 1 77883147 . G C . PASS 1 79355581 . A T . PASS 1 89521878 . T C . PASS 1 100671860 . AT A . PASS 1 110735165 . G A . PASS 1 115604725 . A C . PASS 1 118488548 . A G . PASS 1 120471809 . C A . PASS 1 120612340 . C G . PASS 1 145017837 . CTTCCTTCCTT C . PASS 1 151810924 . G A . PASS 1 156639990 . C T . PASS 1 158613108 . T C . PASS 1 160106522 . AA TT . PASS 1 161009918 . C T . PASS 1 165738001 . TC AA . PASS Thanks in advance for your help! DP=54;ECNT=2;NLOD=4.82;N_ART_LOD=-1.326e+00;POP_AF=1.231e-04;P_CONTAM=7.950e-09;P_GERMLINE=-2.546e+00;TLOD=9.59 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/1:7,4:0.444:3,3:4,1:30,23:166,219:60:6:0|1:2288807_A_C:0.00,0.364,0.364:0.026,0.025,0.949 DP=211;ECNT=1;NLOD=27.99;N_ART_LOD=-1.975e+00;POP_AF=2.462e-05;P_CONTAM=6.191e-11;P_GERMLINE=-5.000e+01;TLOD=10.12 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:110,7:0.065:57,5:53,2:25,32:172,144:60:14:0.040,0.061,0.060:8.086e-03,0.011,0.981 DP=228;ECNT=1;NLOD=27.69;N_ART_LOD=-1.984e+00;POP_AF=2.461e-05;P_CONTAM=0.00;P_GERMLINE=-2.649e+01;TLOD=188.90 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:47,63:0.559:23,37:24,26:26,33:164,156:60:16:0.545,0.556,0.573:0.022,0.018,0.960 DP=40;ECNT=1;NLOD=5.12;N_ART_LOD=-1.255e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-4.891e+00;TLOD=46.65 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 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GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/1:8,3:0.273:8,2:0,1:32,30:165,262:60:13:0|1:115604725_A_C:0.00,0.273,0.273:0.032,0.019,0.949 DP=36;ECNT=1;NLOD=3.91;N_ART_LOD=-1.146e+00;POP_AF=2.500e-06;P_CONTAM=5.738e-06;P_GERMLINE=-6.267e+00;TLOD=6.10 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:20,3:0.131:12,1:8,2:32,31:209,152:60:28:0.00,0.131,0.130:0.024,0.015,0.961 DP=252;ECNT=1;NLOD=31.77;N_ART_LOD=-2.030e+00;POP_AF=2.500e-06;P_CONTAM=3.204e-11;P_GERMLINE=-6.195e+01;TLOD=13.16 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:136,7:0.056:64,4:72,3:32,34:173,145:60:20:0.040,0.040,0.049:8.985e-03,4.997e-03,0.986 DP=106;ECNT=2;NLOD=9.33;N_ART_LOD=-1.517e+00;POP_AF=2.709e-04;P_CONTAM=1.336e-06;P_GERMLINE=-2.036e+01;TLOD=11.08 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:67,5:0.079:39,3:28,2:30,36:246,236:40:24:0.071,0.00,0.069:0.025,0.010,0.964 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0/1:40,4:0.125:19,4:21,0:34,25:185,192:60:27:0.081,0.040,0.091:6.133e-03,0.045,0.948 DP=383;ECNT=1;NLOD=55.38;N_ART_LOD=-2.279e+00;POP_AF=2.500e-06;P_CONTAM=3.582e-04;P_GERMLINE=-1.026e+02;TLOD=7.01 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:183,4:0.023:93,0:90,4:34,34:185,141:60:19:0.020,0.020,0.021:6.809e-03,2.756e-03,0.990 DP=96;ECNT=1;NLOD=7.53;N_ART_LOD=-1.422e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.331e+01;TLOD=29.79 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:57,13:0.187:30,7:27,6:32,31:211,232:60:13:0.162,0.162,0.186:0.053,7.608e-03,0.939 DP=214;ECNT=1;NLOD=17.46;N_ART_LOD=-1.774e+00;POP_AF=2.500e-06;P_CONTAM=6.150e-11;P_GERMLINE=-5.103e+01;TLOD=16.97 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:148,7:0.045:76,4:72,3:31,33:175,170:60:7:0.030,0.040,0.045:0.015,3.328e-03,0.981

Best, Stefan

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atomiuk commented 6 years ago

Hi Andrew, Thanks for your swift reply. I downloaded the current version of dbNSFP.pm by wget https://github.com/Ensembl/VEP_plugins/blob/release/93/dbNSFP.pm but this did not change the error :-(

Kind regards, Stefan

Von: Andrew Parton [mailto:notifications@github.com] Gesendet: Friday, August 24, 2018 11:43 AM An: Ensembl/ensembl-vep ensembl-vep@noreply.github.com Cc: Stefan Tomiuk StefanT@miltenyibiotec.de; Author author@noreply.github.com Betreff: Re: [Ensembl/ensembl-vep] dbNSFP plugin - GRCh37 (#267)

Hi Stefan,

Could you please update your dbNSFP.pm file to the latest version and try again? We updated dbNSFP recently, and that should hopefully fix your issue.

Kind Regards, Andrew

On 24 Aug 2018, at 10:22, atomiuk notifications@github.com<mailto:notifications@github.com> wrote:

Hi, when calling VEP with the dbNSFP plugin as follows

/data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep --species homo_sapiens --input_file test.vcf --output_file ouput.txt --dir_cache /data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep_data/ --offline --tab --assembly GRCh37 --fasta /data2/NGS/pipeline_data_GATK/b37/human_g1k_v37_decoy.fasta --force_overwrite --plugin dbNSFP,dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

I get the error message Use of uninitialized value in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 197. Use of uninitialized value in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 197.

Two columns named aaref and genename are added to the output, but their content is always "-".

For generating the dbNSFPv3.5a file for GRCh37 is used the following commands:

unzip dbNSFPv3.5a.zip head -n1 dbNSFP3.5a_variant.chr1 > h cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz tabix -s 8 -b 9 -e 9 dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz

I tested some of the variants with tabix, e.g. tabix dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz 1:3703503-3703502 and got the expected output.

I used the following VCF as input:

fileformat=VCFv4.2

FILTER=

FILTER=

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FILTER=

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FILTER=

FILTER=

FILTER=

FILTER=

FILTER=

FILTER=

FILTER=

FILTER=

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FORMAT=

GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output somatic_mutect2_w_interval_filtered.vcf.gz --contamination-table 62419341_matched_calculatecontamination.table --variant somatic_mutect2_w_interval.vcf.gz --log-somatic-prior -6.0 --tumor-lod 5.3 --normal-artifact-lod 0.0 --normal-p-value-threshold 0.001 --max-germline-posterior 0.1 --max-alt-allele-count 1 --min-pcr-slippage-size 8 --pcr-slippage-rate 0.1 --pcr-slippage-p-value 0.001 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 5 --max-events-in-region 2 --max-strand-artifact-probability 0.99 --min-strand-artifact-allele-fraction 0.01 --max-contamination-probability 0.1 --unique-alt-read-count 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false",Version=4.0.7.0,Date="August 13, 2018 7:23:01 AM CEST">

GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample 62419341_S1 --normal-sample 62432268_S85 --panel-of-normals /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/PON/PON_centogene_5samples_wo_interval.vcf.gz --germline-resource /data2/NGS/pipeline_data_GATK/b37/af-only-gnomad.raw.sites.b37.vcf.gz --af-of-alleles-not-in-resource 2.5E-6 --bam-output somatic_mutect2_w_interval.bam --output somatic_mutect2_w_interval.vcf.gz --intervals /data2/NGS/SURESELECT/SureSelect_Human_All_Exon_V6_r2/S07604514_Padded_wo_chr.bed --input /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/piped/62419341_recal.bam --input /data2/NGS/PiCoP/GATK/tutorial_data/STEFANM/piped/62432268_recal.bam --reference /data2/NGS/pipeline_data_GATK/b37/human_g1k_v37_decoy.fasta --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter --genotype-pon-sites false --genotype-germline-sites false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --max-mnp-distance 1 --ignore-itr-artifacts false --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --recover-dangling-heads false --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 10.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --disable-tool-default-read-filters false --minimum-mapping-quality 20 --max-read-length 2147483647 --min-read-length 30 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.7.0,Date="August 10, 2018 8:14:24 PM CEST">

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Mutect Version=2.1

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filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.

normal_sample=62432268_S85

source=FilterMutectCalls

source=Mutect2

tumor_sample=62419341_S1

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 62419341_S1

1 2288813 . A C . PASS DP=54;ECNT=2;NLOD=4.82;N_ART_LOD=-1.326e+00;POP_AF=1.231e-04;P_CONTAM=7.950e-09;P_GERMLINE=-2.546e+00;TLOD=9.59 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/1:7,4:0.444:3,3:4,1:30,23:166,219:60:6:0|1:2288807_A_C:0.00,0.364,0.364:0.026,0.025,0.949 1 3319365 . G A . PASS DP=211;ECNT=1;NLOD=27.99;N_ART_LOD=-1.975e+00;POP_AF=2.462e-05;P_CONTAM=6.191e-11;P_GERMLINE=-5.000e+01;TLOD=10.12 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:110,7:0.065:57,5:53,2:25,32:172,144:60:14:0.040,0.061,0.060:8.086e-03,0.011,0.981 1 3703502 . G A . PASS DP=228;ECNT=1;NLOD=27.69;N_ART_LOD=-1.984e+00;POP_AF=2.461e-05;P_CONTAM=0.00;P_GERMLINE=-2.649e+01;TLOD=188.90 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:47,63:0.559:23,37:24,26:26,33:164,156:60:16:0.545,0.556,0.573:0.022,0.018,0.960 1 6196558 . C A . PASS DP=40;ECNT=1;NLOD=5.12;N_ART_LOD=-1.255e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-4.891e+00;TLOD=46.65 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:8,15:0.656:6,7:2,8:35,34:243,202:60:12:0.00,0.657,0.652:0.030,0.025,0.946 1 16892365 . C G . PASS DP=135;ECNT=1;NLOD=16.25;N_ART_LOD=-1.744e+00;POP_AF=2.500e-06;P_CONTAM=7.325e-11;P_GERMLINE=-2.981e+01;TLOD=9.52 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:72,6:0.090:46,3:26,3:36,38:228,252:34:15:0.071,0.020,0.077:1.394e-04,0.945,0.055 1 23768482 . G T . PASS DP=68;ECNT=1;NLOD=9.29;N_ART_LOD=-1.521e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-9.531e+00;TLOD=78.37 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:11,23:0.676:5,15:6,8:31,34:261,213:60:10:0.636,0.667,0.676:0.029,0.022,0.948 1 28834054 . C G . PASS DP=76;ECNT=1;NLOD=5.42;N_ART_LOD=-1.279e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-5.263e+00;TLOD=74.78 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:35,23:0.400:19,17:16,6:31,36:185,171:60:15:0.394,0.354,0.397:0.031,0.020,0.949 1 35885282 . G A . PASS DP=108;ECNT=1;NLOD=11.39;N_ART_LOD=-1.622e+00;POP_AF=2.500e-06;P_CONTAM=2.604e-04;P_GERMLINE=-2.310e+01;TLOD=5.54 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:56,3:0.083:21,1:35,2:36,35:169,181:60:9:0.051,0.00,0.051:0.011,0.012,0.977 1 45810775 . G A . PASS DP=473;ECNT=1;NLOD=44.55;N_ART_LOD=-2.174e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-6.374e+01;TLOD=210.83 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:241,75:0.246:127,39:114,36:26,34:180,168:60:13:0.212,0.232,0.237:0.022,5.412e-03,0.972 1 46495103 . A G . PASS DP=131;ECNT=1;NLOD=13.55;N_ART_LOD=-1.663e+00;POP_AF=2.461e-05;P_CONTAM=0.00;P_GERMLINE=-2.020e+01;TLOD=28.06 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:66,13:0.194:32,9:34,4:34,30:160,164:60:20:0.131,0.152,0.165:0.016,0.012,0.972 1 46876343 . C T . PASS DP=47;ECNT=1;NLOD=7.83;N_ART_LOD=-1.431e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-7.646e+00;TLOD=39.46 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:7,14:0.657:4,7:3,7:36,31:209,228:60:23:0.00,0.667,0.667:0.063,0.016,0.921 1 59247747 . T C . PASS DP=150;ECNT=1;NLOD=13.80;N_ART_LOD=-1.671e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.310e+01;TLOD=167.75 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:52,52:0.500:25,24:27,28:34,36:169,174:60:20:0.475,0.485,0.500:0.017,0.021,0.962 1 64624767 . C T . PASS DP=101;ECNT=1;NLOD=10.84;N_ART_LOD=-1.568e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.709e+01;TLOD=24.19 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:53,10:0.181:30,6:23,4:25,33:173,165:60:13:0.141,0.131,0.159:9.859e-03,0.021,0.969 1 77883147 . G C . PASS DP=16;ECNT=1;NLOD=2.41;N_ART_LOD=-9.542e-01;POP_AF=2.500e-06;P_CONTAM=1.136e-04;P_GERMLINE=-2.168e+00;TLOD=6.15 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:6,2:0.250:2,1:4,1:31,38:223,307:60:18:0.00,0.253,0.250:0.023,0.025,0.952 1 79355581 . A T . PASS DP=38;ECNT=1;NLOD=4.52;N_ART_LOD=-1.204e+00;POP_AF=2.500e-06;P_CONTAM=8.891e-15;P_GERMLINE=-5.011e+00;TLOD=16.90 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:17,6:0.265:8,2:9,4:33,34:193,134:60:21:0.263,0.00,0.261:0.019,0.031,0.951 1 89521878 . T C . PASS DP=83;ECNT=1;NLOD=9.28;N_ART_LOD=-1.504e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.002e+01;TLOD=41.01 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:34,16:0.327:18,3:16,13:32,31:195,203:50:28:0.313,0.273,0.320:0.033,0.018,0.950 1 100671860 . AT A . PASS DP=80;ECNT=1;NLOD=5.71;N_ART_LOD=-1.379e+00;POP_AF=0.012;P_CONTAM=4.575e-07;P_GERMLINE=-4.280e+00;RPA=6,5;RU=T;STR;TLOD=5.95 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:27,5:0.287:12,1:15,4:25,32:217,188:60:20:0.152,0.111,0.156:0.014,0.022,0.964 1 110735165 . G A . PASS DP=215;ECNT=1;NLOD=17.46;N_ART_LOD=-1.777e+00;POP_AF=2.462e-05;P_CONTAM=0.00;P_GERMLINE=-1.650e+01;TLOD=181.04 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:82,60:0.433:40,33:42,27:26,33:172,168:60:13:0.384,0.414,0.423:0.023,0.015,0.962 1 115604725 . A C . PASS DP=27;ECNT=2;NLOD=4.81;N_ART_LOD=-1.230e+00;POP_AF=3.692e-04;P_CONTAM=3.966e-05;P_GERMLINE=-2.455e+00;TLOD=9.75 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/1:8,3:0.273:8,2:0,1:32,30:165,262:60:13:0|1:115604725_A_C:0.00,0.273,0.273:0.032,0.019,0.949 1 118488548 . A G . PASS DP=36;ECNT=1;NLOD=3.91;N_ART_LOD=-1.146e+00;POP_AF=2.500e-06;P_CONTAM=5.738e-06;P_GERMLINE=-6.267e+00;TLOD=6.10 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:20,3:0.131:12,1:8,2:32,31:209,152:60:28:0.00,0.131,0.130:0.024,0.015,0.961 1 120471809 . C A . PASS DP=252;ECNT=1;NLOD=31.77;N_ART_LOD=-2.030e+00;POP_AF=2.500e-06;P_CONTAM=3.204e-11;P_GERMLINE=-6.195e+01;TLOD=13.16 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:136,7:0.056:64,4:72,3:32,34:173,145:60:20:0.040,0.040,0.049:8.985e-03,4.997e-03,0.986 1 120612340 . C G . PASS DP=106;ECNT=2;NLOD=9.33;N_ART_LOD=-1.517e+00;POP_AF=2.709e-04;P_CONTAM=1.336e-06;P_GERMLINE=-2.036e+01;TLOD=11.08 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:67,5:0.079:39,3:28,2:30,36:246,236:40:24:0.071,0.00,0.069:0.025,0.010,0.964 1 145017837 . CTTCCTTCCTT C . PASS DP=44;ECNT=2;NLOD=3.01;N_ART_LOD=-1.041e+00;POP_AF=1.240e-04;P_CONTAM=8.572e-12;P_GERMLINE=-3.970e+00;TLOD=19.33 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:PGT:PID:SA_MAP_AF:SA_POST_PROB 0/1:28,6:0.176:16,3:12,3:37,32:181,122:60:11:0|1:145017837_CTTCCTTCCTT_C:0.172,0.00,0.176:7.833e-05,0.983,0.017 1 151810924 . G A . PASS DP=305;ECNT=1;NLOD=25.44;N_ART_LOD=-1.932e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-5.923e+01;TLOD=34.27 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:185,18:0.110:97,14:88,4:26,33:181,156:60:14:0.020,0.091,0.089:0.490,1.062e-03,0.509 1 156639990 . C T . PASS DP=233;ECNT=1;NLOD=15.65;N_ART_LOD=-1.766e+00;POP_AF=2.500e-06;P_CONTAM=1.124e-15;P_GERMLINE=-4.392e+01;TLOD=18.73 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:140,9:0.115:81,4:59,5:32,34:174,201:60:25:0.061,0.040,0.060:3.221e-03,0.026,0.970 1 158613108 . T C . PASS DP=80;ECNT=1;NLOD=8.98;N_ART_LOD=-1.502e+00;POP_AF=2.500e-06;P_CONTAM=2.464e-07;P_GERMLINE=-1.559e+01;TLOD=6.21 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:40,4:0.125:19,4:21,0:34,25:185,192:60:27:0.081,0.040,0.091:6.133e-03,0.045,0.948 1 160106522 . AA TT . PASS DP=383;ECNT=1;NLOD=55.38;N_ART_LOD=-2.279e+00;POP_AF=2.500e-06;P_CONTAM=3.582e-04;P_GERMLINE=-1.026e+02;TLOD=7.01 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:183,4:0.023:93,0:90,4:34,34:185,141:60:19:0.020,0.020,0.021:6.809e-03,2.756e-03,0.990 1 161009918 . C T . PASS DP=96;ECNT=1;NLOD=7.53;N_ART_LOD=-1.422e+00;POP_AF=2.500e-06;P_CONTAM=0.00;P_GERMLINE=-1.331e+01;TLOD=29.79 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:57,13:0.187:30,7:27,6:32,31:211,232:60:13:0.162,0.162,0.186:0.053,7.608e-03,0.939 1 165738001 . TC AA . PASS DP=214;ECNT=1;NLOD=17.46;N_ART_LOD=-1.774e+00;POP_AF=2.500e-06;P_CONTAM=6.150e-11;P_GERMLINE=-5.103e+01;TLOD=16.97 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:148,7:0.045:76,4:72,3:31,33:175,170:60:7:0.030,0.040,0.045:0.015,3.328e-03,0.981 Thanks in advance for your help!

Best, Stefan

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at7 commented 6 years ago

I used your input data for testing and the dbNSFP plugin writes results to your output but only for variants of type: missens_variants, stop_lost, stop_gained or start_lost. e.g. 1_110735165_G/A 1:110735165 A ENSG00000197106 ENST00000331565 Transcript missense_variant 1629 1144 382 V/I Gtc/Atc - MODERATE - 1 - V SLC6A17

atomiuk commented 6 years ago

this is my output. I have the additional two columns but they don´t have any content :-(

Von: Anja Thormann [mailto:notifications@github.com] Gesendet: Friday, August 24, 2018 1:53 PM An: Ensembl/ensembl-vep ensembl-vep@noreply.github.com Cc: Stefan Tomiuk StefanT@miltenyibiotec.de; Author author@noreply.github.com Betreff: Re: [Ensembl/ensembl-vep] dbNSFP plugin - GRCh37 (#267)

I used your input data for testing and the dbNSFP plugin writes results to your output but only for variants of type: missens_variants, stop_lost, stop_gained or start_lost. e.g. 1_110735165_G/A 1:110735165 A ENSG00000197106 ENST00000331565 Transcript missense_variant 1629 1144 382 V/I Gtc/Atc - MODERATE - 1 - V SLC6A17

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ENSEMBL VARIANT EFFECT PREDICTOR v93.2

Output produced at 2018-08-24 12:42:42

Using cache in /data2/NGS/pipeline_data_GATK/snp/ensembl-vep/vep_data/homo_sapiens/93_GRCh37

Using API version 93, DB version ?

ensembl-variation version 93.c9c43a7

ensembl-funcgen version 93.0c98373

ensembl version 93.b4d45ee

ensembl-io version 93.cc29a66

HGMD-PUBLIC version 20164

dbSNP version 150

genebuild version 2011-04

sift version sift5.2.2

gnomAD version 170228

1000genomes version phase3

polyphen version 2.2.2

ESP version 20141103

regbuild version 1.0

ClinVar version 201706

COSMIC version 81

assembly version GRCh37.p13

gencode version GENCODE 19

Column descriptions:

Uploaded_variation : Identifier of uploaded variant

Location : Location of variant in standard coordinate format (chr:start or chr:start-end)

Allele : The variant allele used to calculate the consequence

Gene : Stable ID of affected gene

Feature : Stable ID of feature

Feature_type : Type of feature - Transcript, RegulatoryFeature or MotifFeature

Consequence : Consequence type

cDNA_position : Relative position of base pair in cDNA sequence

CDS_position : Relative position of base pair in coding sequence

Protein_position : Relative position of amino acid in protein

Amino_acids : Reference and variant amino acids

Codons : Reference and variant codon sequence

Existing_variation : Identifier(s) of co-located known variants

IMPACT : Subjective impact classification of consequence type

DISTANCE : Shortest distance from variant to transcript

STRAND : Strand of the feature (1/-1)

FLAGS : Transcript quality flags

aaref : aaref from dbNSFP file

genename : genename from dbNSFP file

Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS aaref genename

1_2288813_A/C 1:2288813 C ENSG00000116151 ENST00000378529 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_2288813_A/C 1:2288813 C ENSG00000116151 ENST00000378531 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_2288813_A/C 1:2288813 C ENSG00000269896 ENST00000602865 Transcript upstream_gene_variant - - - - - - MODIFIER 4554 -1 - - - 1_2288813_A/C 1:2288813 C ENSG00000116151 ENST00000606372 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_2288813_A/C 1:2288813 C ENSG00000116151 ENST00000607342 Transcript downstream_gene_variant - - - - - - MODIFIER 1264 -1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000270722 Transcript synonymous_variant 736 687 229 T acG/acA - LOW - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000378391 Transcript synonymous_variant 750 687 229 T acG/acA - LOW - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000378398 Transcript synonymous_variant 772 690 230 T acG/acA - LOW - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000441472 Transcript synonymous_variant 769 687 229 T acG/acA - LOW - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000442529 Transcript synonymous_variant 769 687 229 T acG/acA - LOW - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000509860 Transcript synonymous_variant 114 114 38 T acG/acA - LOW - 1 cds_start_NF - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000511072 Transcript synonymous_variant 782 690 230 T acG/acA - LOW - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000512462 Transcript non_coding_transcript_exon_variant 465 - - - - - MODIFIER - 1 - - - 1_3319365_G/A 1:3319365 A ENSG00000142611 ENST00000514189 Transcript synonymous_variant 739 690 230 T acG/acA - LOW - 1 - - - 1_3703502_G/A 1:3703502 A ENSG00000130764 ENST00000378251 Transcript missense_variant 1016 988 330 R/W Cgg/Tgg - MODERATE - -1 - - - 1_3703502_G/A 1:3703502 A ENSG00000130764 ENST00000462356 Transcript upstream_gene_variant - - - - - - MODIFIER 2763 -1 - - - 1_3703502_G/A 1:3703502 A ENSG00000130764 ENST00000479239 Transcript upstream_gene_variant - - - - - - MODIFIER 2891 -1 cds_start_NF - - 1_3703502_G/A 1:3703502 A ENSG00000266075 ENST00000581512 Transcript downstream_gene_variant - - - - - - MODIFIER 3829 1 - - - 1_3703502_G/A 1:3703502 A ENSG00000272153 ENST00000607459 Transcript downstream_gene_variant - - - - - - MODIFIER 1400 1 - - - 1_6196558_C/A 1:6196558 A ENSG00000116254 ENST00000262450 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_6196558_C/A 1:6196558 A ENSG00000116254 ENST00000377999 Transcript upstream_gene_variant - - - - - - MODIFIER 4759 -1 cds_start_NF - - 1_6196558_C/A 1:6196558 A ENSG00000116254 ENST00000378021 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_6196558_C/A 1:6196558 A ENSG00000116254 ENST00000462991 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 cds_start_NF - - 1_6196558_C/A 1:6196558 A ENSG00000116254 ENST00000496404 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_16892365_C/G 1:16892365 G ENSG00000219481 ENST00000287968 Transcript downstream_gene_variant - - - - - - MODIFIER 3218 -1 - - - 1_16892365_C/G 1:16892365 G ENSG00000219481 ENST00000392963 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_16892365_C/G 1:16892365 G ENSG00000219481 ENST00000420031 Transcript downstream_gene_variant - - - - - - MODIFIER 570 -1 - - - 1_16892365_C/G 1:16892365 G ENSG00000219481 ENST00000430580 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_16892365_C/G 1:16892365 G ENSG00000219481 ENST00000432949 Transcript downstream_gene_variant - - - - - - MODIFIER 570 -1 - - - 1_23768482_G/T 1:23768482 T ENSG00000088280 ENST00000336689 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_23768482_G/T 1:23768482 T ENSG00000088280 ENST00000437606 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_23768482_G/T 1:23768482 T ENSG00000088280 ENST00000475814 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 cds_start_NF - - 1_23768482_G/T 1:23768482 T ENSG00000088280 ENST00000478858 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_23768482_G/T 1:23768482 T ENSG00000088280 ENST00000492982 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_23768482_G/T 1:23768482 T ENSG00000088280 ENST00000530874 Transcript upstream_gene_variant - - - - - - MODIFIER 2973 -1 - - - 1_28834054_C/G 1:28834054 G ENSG00000200087 ENST00000363217 Transcript upstream_gene_variant - - - - - - MODIFIER 1017 1 - - - 1_28834054_C/G 1:28834054 G ENSG00000242125 ENST00000364938 Transcript non_coding_transcript_exon_variant 177 - - - - - MODIFIER - 1 - - - 1_28834054_C/G 1:28834054 G ENSG00000180198 ENST00000373833 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_28834054_C/G 1:28834054 G ENSG00000180198 ENST00000398958 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_28834054_C/G 1:28834054 G ENSG00000242125 ENST00000413987 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_28834054_C/G 1:28834054 G ENSG00000180198 ENST00000419074 Transcript upstream_gene_variant - - - - - - MODIFIER 2535 1 cds_end_NF - - 1_28834054_C/G 1:28834054 G ENSG00000180198 ENST00000427469 Transcript intron_variant - - - - - - MODIFIER - 1 cds_end_NF - - 1_28834054_C/G 1:28834054 G ENSG00000180198 ENST00000434290 Transcript intron_variant - - - - - - MODIFIER - 1 cds_end_NF - - 1_28834054_C/G 1:28834054 G ENSG00000242125 ENST00000437681 Transcript non_coding_transcript_exon_variant 1192 - - - - - MODIFIER - 1 - - - 1_28834054_C/G 1:28834054 G ENSG00000242125 ENST00000447507 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_35885282_G/A 1:35885282 A ENSG00000146463 ENST00000314607 Transcript 3_prime_UTR_variant 4731 - - - - - MODIFIER - 1 - - - 1_35885282_G/A 1:35885282 A ENSG00000146463 ENST00000373297 Transcript 3_prime_UTR_variant 4464 - - - - - MODIFIER - 1 - - - 1_35885282_G/A 1:35885282 A ENSG00000146463 ENST00000457946 Transcript 3_prime_UTR_variant 3626 - - - - - MODIFIER - 1 cds_start_NF - - 1_45810775_G/A 1:45810775 A ENSG00000070759 ENST00000341771 Transcript missense_variant 1769 1366 456 R/C Cgc/Tgc - MODERATE - -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000355498 Transcript upstream_gene_variant - - - - - - MODIFIER 4988 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000070759 ENST00000372084 Transcript missense_variant 1380 1366 456 R/C Cgc/Tgc - MODERATE - -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000070759 ENST00000372086 Transcript missense_variant 1854 1453 485 R/C Cgc/Tgc - MODERATE - -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132773 ENST00000372090 Transcript downstream_gene_variant - - - - - - MODIFIER 1128 1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000372098 Transcript upstream_gene_variant - - - - - - MODIFIER 4715 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000372100 Transcript upstream_gene_variant - - - - - - MODIFIER 4988 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000372110 Transcript upstream_gene_variant - - - - - - MODIFIER 4715 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000372115 Transcript upstream_gene_variant - - - - - - MODIFIER 4633 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000412971 Transcript upstream_gene_variant - - - - - - MODIFIER 4722 -1 cds_end_NF - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000450313 Transcript upstream_gene_variant - - - - - - MODIFIER 4633 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132773 ENST00000460057 Transcript downstream_gene_variant - - - - - - MODIFIER 2244 1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000461495 Transcript upstream_gene_variant - - - - - - MODIFIER 4688 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000462387 Transcript upstream_gene_variant - - - - - - MODIFIER 4671 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000467940 Transcript upstream_gene_variant - - - - - - MODIFIER 4716 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132773 ENST00000471337 Transcript downstream_gene_variant - - - - - - MODIFIER 2125 1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000476789 Transcript upstream_gene_variant - - - - - - MODIFIER 4671 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132773 ENST00000477731 Transcript downstream_gene_variant - - - - - - MODIFIER 2342 1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000481139 Transcript upstream_gene_variant - - - - - - MODIFIER 4688 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000481571 Transcript upstream_gene_variant - - - - - - MODIFIER 4715 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000483642 Transcript upstream_gene_variant - - - - - - MODIFIER 4706 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000070759 ENST00000486676 Transcript non_coding_transcript_exon_variant 1800 - - - - - MODIFIER - -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132773 ENST00000495703 Transcript downstream_gene_variant - - - - - - MODIFIER 1139 1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000525160 Transcript upstream_gene_variant - - - - - - MODIFIER 4689 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000528332 Transcript upstream_gene_variant - - - - - - MODIFIER 4656 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000529984 Transcript upstream_gene_variant - - - - - - MODIFIER 4656 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000531105 Transcript upstream_gene_variant - - - - - - MODIFIER 4940 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132781 ENST00000534453 Transcript upstream_gene_variant - - - - - - MODIFIER 4868 -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000070759 ENST00000538496 Transcript missense_variant 1523 1204 402 R/C Cgc/Tgc - MODERATE - -1 - - - 1_45810775_G/A 1:45810775 A ENSG00000132773 ENST00000539779 Transcript downstream_gene_variant - - - - - - MODIFIER 1344 1 - - - 1_46495103_A/G 1:46495103 G ENSG00000086015 ENST00000361297 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_46495103_A/G 1:46495103 G ENSG00000086015 ENST00000372008 Transcript intron_variant - - - - - - MODIFIER - 1 cds_end_NF - - 1_46495103_A/G 1:46495103 G ENSG00000086015 ENST00000372009 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_46495103_A/G 1:46495103 G ENSG00000086015 ENST00000477968 Transcript non_coding_transcript_exon_variant 267 - - - - - MODIFIER - 1 - - - 1_46495103_A/G 1:46495103 G ENSG00000086015 ENST00000492813 Transcript upstream_gene_variant - - - - - - MODIFIER 4437 1 - - - 1_46876343_C/T 1:46876343 T ENSG00000117480 ENST00000243167 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_46876343_C/T 1:46876343 T ENSG00000117480 ENST00000468718 Transcript downstream_gene_variant - - - - - - MODIFIER 4882 1 - - - 1_46876343_C/T 1:46876343 T ENSG00000117480 ENST00000484697 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_46876343_C/T 1:46876343 T ENSG00000117480 ENST00000489366 Transcript downstream_gene_variant - - - - - - MODIFIER 1383 1 - - - 1_46876343_C/T 1:46876343 T ENSG00000117480 ENST00000493636 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_46876343_C/T 1:46876343 T ENSG00000117480 ENST00000493735 Transcript downstream_gene_variant - - - - - - MODIFIER 1473 1 - - - 1_59247747_T/C 1:59247747 C ENSG00000177606 ENST00000371222 Transcript stop_lost 2039 996 332 */W tgA/tgG - HIGH - -1 - - - 1_59247747_T/C 1:59247747 C ENSG00000234807 ENST00000419531 Transcript upstream_gene_variant - - - - - - MODIFIER 3085 1 - - - 1_59247747_T/C 1:59247747 C ENSG00000234807 ENST00000544621 Transcript upstream_gene_variant - - - - - - MODIFIER 3076 1 - - - 1_64624767_C/T 1:64624767 T ENSG00000185483 ENST00000371079 Transcript synonymous_variant 1653 1278 426 C tgC/tgT - LOW - 1 - - - 1_64624767_C/T 1:64624767 T ENSG00000223949 ENST00000424995 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_64624767_C/T 1:64624767 T ENSG00000185483 ENST00000545203 Transcript 5_prime_UTR_variant 919 - - - - - MODIFIER - 1 - - - 1_77883147_G/C 1:77883147 C ENSG00000154027 ENST00000344720 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_77883147_G/C 1:77883147 C ENSG00000154027 ENST00000354567 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_77883147_G/C 1:77883147 C ENSG00000154027 ENST00000465146 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_77883147_G/C 1:77883147 C ENSG00000251767 ENST00000515958 Transcript upstream_gene_variant - - - - - - MODIFIER 2863 1 - - - 1_77883147_G/C 1:77883147 C ENSG00000154027 ENST00000527263 Transcript upstream_gene_variant - - - - - - MODIFIER 231 1 cds_start_NF - - 1_77883147_G/C 1:77883147 C ENSG00000154027 ENST00000530826 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_79355581_A/T 1:79355581 T ENSG00000162618 ENST00000370742 Transcript 3_prime_UTR_variant 3395 - - - - - MODIFIER - -1 - - - 1_79355581_A/T 1:79355581 T ENSG00000162618 ENST00000401034 Transcript intron_variant - - - - - - MODIFIER - -1 cds_start_NF - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000370473 Transcript missense_variant 1409 1189 397 K/E Aaa/Gaa - MODERATE - -1 - - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000459831 Transcript downstream_gene_variant - - - - - - MODIFIER 2146 -1 - - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000468959 Transcript upstream_gene_variant - - - - - - MODIFIER 136 -1 - - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000479889 Transcript upstream_gene_variant - - - - - - MODIFIER 818 -1 - - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000484970 Transcript upstream_gene_variant - - - - - - MODIFIER 854 -1 - - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000493139 Transcript downstream_gene_variant - - - - - - MODIFIER 2795 -1 - - - 1_89521878_T/C 1:89521878 C ENSG00000117228 ENST00000495131 Transcript non_coding_transcript_exon_variant 122 - - - - - MODIFIER - -1 - - - 1_100671861_T/- 1:100671861 - ENSG00000137992 ENST00000370131 Transcript downstream_gene_variant - - - - - - MODIFIER 4238 -1 - - - 1_100671861_T/- 1:100671861 - ENSG00000137992 ENST00000370132 Transcript splice_region_variant,intron_variant - - - - - - LOW - -1 - - - 1_110735165_G/A 1:110735165 A ENSG00000197106 ENST00000331565 Transcript missense_variant 1629 1144 382 V/I Gtc/Atc - MODERATE - 1 - - - 1_110735165_G/A 1:110735165 A ENSG00000197106 ENST00000465159 Transcript upstream_gene_variant - - - - - - MODIFIER 25 1 - - - 1_115604725_A/C 1:115604725 C ENSG00000134198 ENST00000369514 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_115604725_A/C 1:115604725 C ENSG00000134198 ENST00000369515 Transcript intron_variant - - - - - - MODIFIER - -1 cds_start_NF,cds_end_NF - - 1_115604725_A/C 1:115604725 C ENSG00000134198 ENST00000369516 Transcript intron_variant - - - - - - MODIFIER - -1 cds_start_NF,cds_end_NF - - 1_115604725_A/C 1:115604725 C ENSG00000134198 ENST00000433172 Transcript intron_variant - - - - - - MODIFIER - -1 cds_start_NF,cds_end_NF - - 1_115604725_A/C 1:115604725 C ENSG00000134198 ENST00000491992 Transcript upstream_gene_variant - - - - - - MODIFIER 3679 -1 cds_start_NF,cds_end_NF - - 1_118488548_A/G 1:118488548 G ENSG00000065183 ENST00000349139 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_118488548_A/G 1:118488548 G ENSG00000065183 ENST00000369441 Transcript downstream_gene_variant - - - - - - MODIFIER 4137 1 - - - 1_120471809_C/A 1:120471809 A ENSG00000134250 ENST00000256646 Transcript missense_variant 3902 3682 1228 D/Y Gac/Tac - MODERATE - -1 - - - 1_120612340_C/G 1:120612340 G ENSG00000134250 ENST00000256646 Transcript upstream_gene_variant - - - - - - MODIFIER 100 -1 - - - 1_120612340_C/G 1:120612340 G ENSG00000134250 ENST00000479412 Transcript upstream_gene_variant - - - - - - MODIFIER 100 -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000313382 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000369348 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000369359 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000478649 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000485062 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000493130 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000496572 Transcript upstream_gene_variant - - - - - - MODIFIER 1900 -1 cds_start_NF - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000497529 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000526359 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000527063 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000528552 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000528661 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000530078 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000530740 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000530822 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000530940 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000531369 Transcript intron_variant - - - - - - MODIFIER - -1 cds_end_NF - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000532801 Transcript intron_variant - - - - - - MODIFIER - -1 cds_end_NF - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000532803 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000533163 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000533259 Transcript intron_variant - - - - - - MODIFIER - -1 cds_end_NF - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000178104 ENST00000533396 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_145017838_TTCCTTCCTT/- 1:145017838-145017847 - ENSG00000272755 ENST00000610119 Transcript upstream_gene_variant - - - - - - MODIFIER 548 1 - - - 1_151810924_G/A 1:151810924 A ENSG00000201134 ENST00000364264 Transcript downstream_gene_variant - - - - - - MODIFIER 3288 -1 - - - 1_151810924_G/A 1:151810924 A ENSG00000234614 ENST00000434182 Transcript upstream_gene_variant - - - - - - MODIFIER 3429 1 - - - 1_151810924_G/A 1:151810924 A ENSG00000225556 ENST00000454109 Transcript missense_variant 1128 542 181 P/L cCg/cTg - MODERATE - -1 - - - 1_156639990_C/T 1:156639990 T ENSG00000132688 ENST00000368223 Transcript synonymous_variant 4123 3990 1330 E gaG/gaA - LOW - -1 - - - 1_158613108_T/C 1:158613108 C ENSG00000163554 ENST00000368147 Transcript splice_region_variant,intron_variant - - - - - - LOW - -1 - - - 1_158613108_T/C 1:158613108 C ENSG00000163554 ENST00000465741 Transcript upstream_gene_variant - - - - - - MODIFIER 786 -1 - - - 1_160106522_AA/TT 1:160106522-160106523 TT ENSG00000018625 ENST00000361216 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_160106522_AA/TT 1:160106522-160106523 TT ENSG00000018625 ENST00000392233 Transcript intron_variant - - - - - - MODIFIER - 1 - - - 1_160106522_AA/TT 1:160106522-160106523 TT ENSG00000018625 ENST00000447527 Transcript intron_variant - - - - - - MODIFIER - 1 cds_start_NF - - 1_160106522_AA/TT 1:160106522-160106523 TT ENSG00000018625 ENST00000459972 Transcript upstream_gene_variant - - - - - - MODIFIER 3226 1 - - - 1_160106522_AA/TT 1:160106522-160106523 TT ENSG00000018625 ENST00000463989 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_160106522_AA/TT 1:160106522-160106523 TT ENSG00000018625 ENST00000472488 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - 1 - - - 1_161009918_C/T 1:161009918 T ENSG00000270149 ENST00000289779 Transcript upstream_gene_variant - - - - - - MODIFIER 1184 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000318289 Transcript upstream_gene_variant - - - - - - MODIFIER 1191 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000368019 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000368020 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000368021 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000368023 Transcript upstream_gene_variant - - - - - - MODIFIER 1178 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000368024 Transcript upstream_gene_variant - - - - - - MODIFIER 1151 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000423014 Transcript upstream_gene_variant - - - - - - MODIFIER 1138 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000435396 Transcript intron_variant - - - - - - MODIFIER - -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000462952 Transcript upstream_gene_variant - - - - - - MODIFIER 1821 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000466967 Transcript upstream_gene_variant - - - - - - MODIFIER 1399 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000270149 ENST00000470694 Transcript upstream_gene_variant - - - - - - MODIFIER 1166 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000472217 Transcript intron_variant,non_coding_transcript_variant - - - - - - MODIFIER - -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000473969 Transcript intron_variant,NMD_transcript_variant - - - - - - MODIFIER - -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000215845 ENST00000486084 Transcript upstream_gene_variant - - - - - - MODIFIER 1212 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000491629 Transcript downstream_gene_variant - - - - - - MODIFIER 1198 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000496363 Transcript downstream_gene_variant - - - - - - MODIFIER 312 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000528768 Transcript intron_variant - - - - - - MODIFIER - -1 cds_start_NF - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000529476 Transcript downstream_gene_variant - - - - - - MODIFIER 1479 -1 - - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000531842 Transcript downstream_gene_variant - - - - - - MODIFIER 81 -1 cds_end_NF - - 1_161009918_C/T 1:161009918 T ENSG00000158773 ENST00000534633 Transcript downstream_gene_variant - - - - - - MODIFIER 1262 -1 cds_end_NF - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000367881 Transcript missense_variant 416-417 140-141 47 R/I aGA/aTT - MODERATE - -1 - - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000392129 Transcript 5_prime_UTR_variant 138-139 - - - - - MODIFIER - -1 - - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000224358 ENST00000423121 Transcript upstream_gene_variant - - - - - - MODIFIER 164 1 - - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000464650 Transcript 5_prime_UTR_variant 112-113 - - - - - MODIFIER - -1 - - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000465705 Transcript missense_variant,NMD_transcript_variant 154-155 140-141 47 R/I aGA/aTT - MODERATE - -1 - - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000476143 Transcript missense_variant,NMD_transcript_variant 124-125 125-126 42 R/I aGA/aTT - MODERATE - -1 cds_start_NF - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000481278 Transcript 5_prime_UTR_variant 73-74 - - - - - MODIFIER - -1 cds_end_NF - - 1_165738001_TC/AA 1:165738001-165738002 AA ENSG00000143183 ENST00000580248 Transcript intron_variant - - - - - - MODIFIER - -1 - - -

at7 commented 6 years ago

Unfortunately, I don't understand why you are not getting any results. I will need a few more information. So when you run tabix dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz 1:3703501-3703502 you do get a result? Do you still get the Use of uninitialized value in concatenation warnings? line 197 is pointing to comments in the version of the plugin that I use (most recent checkout from release/93). Could you also please share your tabix version? Thanks!

atomiuk commented 6 years ago

Please find attached the result of the tabix command. My tabix version is 1.2.1. Yes, I am still getting the concatenation warnings.

Von: Anja Thormann [mailto:notifications@github.com] Gesendet: Friday, August 24, 2018 3:14 PM An: Ensembl/ensembl-vep ensembl-vep@noreply.github.com Cc: Stefan Tomiuk StefanT@miltenyibiotec.de; Author author@noreply.github.com Betreff: Re: [Ensembl/ensembl-vep] dbNSFP plugin - GRCh37 (#267)

Unfortunately, I don't understand why you are not getting any results. I will need a few more information. So when you run tabix dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz 1:3703501-3703502 you do get a result? Do you still get the Use of uninitialized value in concatenation warnings? line 197 is pointing to comments in the version of the plugin that I use (most recent checkout from release/93). Could you also please share your tabix version? Thanks!

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1 3786937 C A R L . 1 3703501 1 3693361 LRRC47 - CGG 2 0 C C/C C/C ENSG00000130764 ENST00000378251 ENSP00000367498 330 0.01 0.56404 D Q8N1G4 LRC47_HUMAN 330 0.208 0.28231 B 0.029 0.20261 B 0.007735 0.31213 N 0.378424 0.999776 0.20400 N simple_aae R330L LRC47_HUMAN R330L 1.445 0.36475 L 1.07 0.39585 T -2.57 0.55457 D NM_020710.2 R330L 0.313 0.37373 -1.0525 0.13695 T 0.0529 0.22424 T 10 0.00994546465272 0.26081 T 0.044 0.12274 0.419 0.46102 Q8N1G4 R330L Loss of MoRF binding (P = 0.072); Loss of disorder (P = 0.0805); Loss of sheet (P = 0.0817); Gain of catalytic residue at R330 (P = 0.0844); Loss of solvent accessibility (P = 0.1922) 2.929709 0.41256 22.0 0.95837326245170507 0.27372 0.39806 0.26061 N AEFBCI c -0.856501806487472 0.576403 -0.865280542788395 0.6674337 0.12726 0.88941177644902 0.25780 0.706548 0.72963 0 0.702456 0.74369 0 0.702456 0.68477 0 0.714379 0.83238 0 5.22 -3.13 0.04915 0.086000 0.14667 -0.171000 0.10530 0.137000 0.23241 0.179000 0.21237 0.0:0.3038:0.0:0.6962 12.528 0.55264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 233420 4.284123e-06 0 13968 0 0 32760 0 0 9556 0 0 16664 0 0 20438 0 1 105364 9.490908e-06 0 29460 0 0 5210 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3786937 C G R P . 1 3703501 1 3693361 LRRC47 - CGG 2 0 C C/C C/C ENSG00000130764 ENST00000378251 ENSP00000367498 330 0.008 0.58573 D Q8N1G4 LRC47_HUMAN 330 0.564 0.36526 P 0.082 0.27574 B 0.007735 0.31213 N 0.378424 0.999762 0.20435 N simple_aae R330P LRC47_HUMAN R330P 1.79 0.46914 L 1.08 0.39400 T -2.83 0.59663 D NM_020710.2 R330P 0.442 0.49626 -1.0452 0.15751 T 0.0563 0.23717 T 10 0.0127316927912 0.31736 T 0.071 0.21181 0.472 0.54757 Q8N1G4 R330P Loss of MoRF binding (P = 0.0613); Loss of sheet (P = 0.0817); Gain of phosphorylation at S326 (P = 0.1303); Gain of helix (P = 0.1736); Gain of disorder (P = 0.1741) 2.713978 0.38719 20.9 0.9701144133257944 0.31430 0.41257 0.26382 N AEFBCI c -0.661146269722669 0.8792253 -0.724619931658515 0.864424 0.16099 0.88941177644902 0.25780 0.706548 0.72963 0 0.702456 0.74369 0 0.702456 0.68477 0 0.714379 0.83238 0 5.22 -3.13 0.04915 0.086000 0.14667 -0.171000 0.10530 0.137000 0.23241 0.179000 0.21237 0.0:0.3038:0.0:0.6962 12.528 0.55264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 3786937 C T R Q rs370495428 1 3703501 1 3693361 LRRC47 - CGG 2 0 C C/C C/C ENSG00000130764 ENST00000378251 ENSP00000367498 330 0.175 0.22366 T Q8N1G4 LRC47_HUMAN 330 0.414 0.33364 B 0.017 0.16985 B 0.007735 0.31213 N 0.378424 0.99997 0.18614 N simple_aae R330Q LRC47_HUMAN R330Q 1.79 0.46914 L 1.09 0.39222 T -0.93 0.24895 N NM_020710.2 R330Q 0.171 0.20712 -1.0419 0.16725 T 0.0468 0.20039 T 10 0.00883403571813 0.23472 T 0.021 0.04163 . . . . . 1.716930 0.26739 14.50 0.98260740826765935 0.39172 0.14075 0.18014 N AEFBCI c -0.815924090196577 0.6320534 -0.839308778022193 0.703231 0.13343 0.88941177644902 0.25780 0.706548 0.72963 0 0.702456 0.74369 0 0.702456 0.68477 0 0.714379 0.83238 0 5.22 -3.13 0.04915 0.086000 0.14667 -0.171000 0.10530 0.137000 0.23241 0.179000 0.21237 0.0:0.3038:0.0:0.6962 12.528 0.55264 . . . . . . . . . . . . . . . . 0 0.0 1 1.1630611770179111E-4 8 6.598e-05 8 1.023e-04 0 0 2 2.675e-04 0 0 0 0 5 1.168e-04 1 8.226e-05 8 7.536e-05 8 1.181e-04 0 0 2 2.762e-04 0 0 0 0 5 1.455e-04 1 8.264e-05 6 6.622e-05 6 9.879e-05 0 0 2 2.677e-04 0 0 0 0 3 1.065e-04 1 8.229e-05 10 233420 4.284123e-05 1 13968 7.159221e-05 2 32760 6.105006e-05 0 9556 0 0 16664 0 0 20438 0 6 105364 5.694545e-05 1 29460 3.394433e-05 0 5210 0 1 30954 3.230600e-05 1 8730 1.145475e-04 0 838 0 0 302 0 0 1622 0 0 3492 0 0 14988 0 0 982 0 . . . . . . . 1 3786938 G A R W rs542812217 1 3703502 1 3693362 LRRC47 - CGG 1 2 G G/G G/G ENSG00000130764 ENST00000378251 ENSP00000367498 330 0.002 0.72092 D Q8N1G4 LRC47_HUMAN 330 0.991 0.62216 D 0.518 0.46313 P 0.007735 0.31213 N 0.378424 0.999238 0.21456 N simple_aae R330W LRC47_HUMAN R330W 1.79 0.46914 L 1.0 0.41394 T -3.47 0.67779 D NM_020710.2 R330W 0.36 0.42116 -1.0048 0.28510 T 0.0679 0.27884 T 10 0.0273749951479 0.50352 D 0.137 0.37492 . . . . . 4.271286 0.57209 24.0 0.99679393924023463 0.79002 0.69066 0.33767 D AEFBCI c -0.363494212280507 1.464147 -0.449267189741022 1.286034 0.23170 0.831490936971036 0.24674 0.706548 0.72963 0 0.702456 0.74369 0 0.702456 0.68477 0 0.714379 0.83238 0 5.22 -2.03 0.06920 2.506000 0.44847 0.135000 0.21895 0.995000 0.38529 0.199000 0.21701 0.1144:0.0684:0.3788:0.4384 4.3108 0.10335 1 1.9968051118210862E-4 1 7.564296520423601E-4 0 0.0 0 0.0 0 0.0 0 0.0 . . . . . . . . 8 6.598e-05 7 8.867e-05 3 4.452e-04 0 0 0 0 0 0 3 6.935e-05 1 8.185e-05 8 7.536e-05 7 1.024e-04 3 5.252e-04 0 0 0 0 0 0 3 8.644e-05 1 8.224e-05 7 7.726e-05 7 1.142e-04 3 4.458e-04 0 0 0 0 0 0 3 1.053e-04 1 8.187e-05 13 233794 5.560451e-05 3 13996 2.143470e-04 3 32784 9.150805e-05 0 9572 0 0 16696 0 0 20420 0 6 105600 5.681818e-05 1 29522 3.387304e-05 0 5204 0 1 30948 3.231227e-05 0 8720 0 0 838 0 0 302 0 0 1622 0 0 3492 0 1 14992 6.670224e-05 0 982 0 . . . . . . . 1 3786938 G C R G . 1 3703502 1 3693362 LRRC47 - CGG 1 2 G G/G G/G ENSG00000130764 ENST00000378251 ENSP00000367498 330 0.09 0.31944 T Q8N1G4 LRC47_HUMAN 330 0.208 0.28231 B 0.029 0.20261 B 0.007735 0.31213 N 0.378424 0.999744 0.20503 N simple_aae R330G LRC47_HUMAN R330G 1.79 0.46914 L 1.04 0.40219 T -3.14 0.63977 D NM_020710.2 R330G 0.195 0.23880 -1.0811 0.07126 T 0.0511 0.21729 T 10 0.0132820776808 0.32738 T 0.048 0.13679 0.4 0.42984 Q8N1G4 R330G Gain of catalytic residue at R330 (P = 0.0379); Gain of helix (P = 0.062); Loss of MoRF binding (P = 0.0766); Loss of solvent accessibility (P = 0.0769); Loss of sheet (P = 0.0817) 1.816362 0.27917 15.08 0.91925688298646946 0.20656 0.68337 0.33491 D AEFBCI c -0.784104525016981 0.6781576 -0.751979396730295 0.8254984 0.15436 0.831490936971036 0.24674 0.706548 0.72963 0 0.702456 0.74369 0 0.702456 0.68477 0 0.714379 0.83238 0 5.22 -2.03 0.06920 2.506000 0.44847 0.135000 0.21895 0.995000 0.38529 0.199000 0.21701 0.1144:0.0684:0.3788:0.4384 4.3108 0.10335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

at7 commented 6 years ago

Could you please specify the full path to your dbNSFP file? --plugin dbNSFP,PATH_TO_FILE/dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

Thanks

atomiuk commented 6 years ago

I tried several paths

Initially, I used a softlink in my working folder on /data2/NGS/pipeline_data_GATK/snp/data/dbNSFPv3.5a/dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz

this produces the concatenation error and empty columns for aaref and genename in the output file

--plugin dbNSFP,dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

I also tried the full path

no concatenation error but still empty columns aaref and genename in the output file

--plugin dbNSFP,/data2/NGS/pipeline_data_GATK/snp/data/dbNSFPv3.5a/dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz copied to the foulder where vep is located: /data2/NGS/pipeline_data_GATK/snp/ensembl-vep

run vep in this folder using full path info in command line

this produces the concatenation error and empty columns for aaref and genename in the output file

--plugin dbNSFP,dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz copied to the foulder where vep is located: /data2/NGS/pipeline_data_GATK/snp/ensembl-vep

run vep in this folder using full path info in command line

in addition to the concatenation errors this returned

Use of uninitialized value $readme_file in concatenation (.) or string at /home/stefant/.vep/Plugins/dbNSFP.pm line 157.

--plugin dbNSFP,/data2/NGS/pipeline_data_GATK/snp/ensembl-vep/dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

Von: Anja Thormann [mailto:notifications@github.com] Gesendet: Friday, August 24, 2018 4:43 PM An: Ensembl/ensembl-vep ensembl-vep@noreply.github.com Cc: Stefan Tomiuk StefanT@miltenyibiotec.de; Author author@noreply.github.com Betreff: Re: [Ensembl/ensembl-vep] dbNSFP plugin - GRCh37 (#267)

Could you please specify the full path to your dbNSFP file? --plugin dbNSFP,PATH_TO_FILE/dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename

Thanks

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at7 commented 6 years ago

The plugin is looking for the readme file (dbNSFP3.5a_grch37.readme.txt) in the same directory which contains the dbNSFP file. If you move all the files (dbNSFP3.5a_grch37.readme.txt, dbNSFP3.5a_grch37.txt.gz and dbNSFP3.5a_grch37.txt.gz.tbi) to the same location it hopefully should work.

atomiuk commented 6 years ago

Dear Anja, Thany you very much for your support!

In the header my output file, there are the lines

aaref : (from dbNSFP) reference amino acid "." if the variant is a splicing site SNP (2bp on each end of an intron)

genename : (from dbNSFP) gene name; if the nsSNV can be assigned to multiple genes, gene names are separated by ";"

which probably indicates that the readme.txt file was recognized and parsed. However, the columns aaref and genename in the output file are still empty ... .

Von: Anja Thormann [mailto:notifications@github.com] Gesendet: Tuesday, August 28, 2018 10:00 AM An: Ensembl/ensembl-vep ensembl-vep@noreply.github.com Cc: Stefan Tomiuk StefanT@miltenyibiotec.de; Author author@noreply.github.com Betreff: Re: [Ensembl/ensembl-vep] dbNSFP plugin - GRCh37 (#267)

The plugin is looking for the readme file (dbNSFP3.5a_grch37.readme.txt) in the same directory which contains the dbNSFP file. If you move all the files (dbNSFP3.5a_grch37.readme.txt, dbNSFP3.5a_grch37.txt.gz and dbNSFP3.5a_grch37.txt.gz.tbi) to the same location it hopefully should work.

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at7 commented 6 years ago

If you have all the required files under /data2/NGS/pipeline_data_GATK/snp/data/dbNSFPv3.5a/ and call the plugin with --plugin dbNSFP,/data2/NGS/pipeline_data_GATK/snp/data/dbNSFPv3.5a/dbNSFP3.5a_GRCh37_for_vep_plugin.txt.gz,aaref,genename and there are no error messages like Failed to instantiate plugin dbNSFP: ERROR: Data file not found or open: No such file or directory [main] fail to open the data file. I really don't understand why you don't get any dbNSFP results. I keep investigating and will get back to you when I find out what might be going on.

at7 commented 4 years ago

Dear @atomiuk, coming back to this issue I still don't know why the annotations are missing from your output file. I was wondering if you could update your code to the latest version 98 and try running VEP with the dbNSFP plugin option again? Best wishes, Anja

at7 commented 4 years ago

I will close this issue now. But please create a new issue or reopen this issue if you still need help with running the plugin.

Ensembl / ensembl-vep

dbNSFP plugin - GRCh37 #267

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