search

mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
Other
373 stars 216 forks source link

Annotate hg19 vcf #29

Closed apastore closed 8 years ago

apastore commented 8 years ago

Hi Cyriac, with the previous version of vcf2maf I had no problem annotating hg19 vcf even with vep 82, but with the current 1.6.3 I am getting this error... I was trying to figure out if zoo make some change but I did not discover something obvious ... do you have some suggestion (except sed/awk)

Thanks! Alessandro

WARNING: Could not fetch sub-slice from 1:888639-888639(1) on line 210 WARNING: Specified reference allele T does not match Ensembl reference allele on line 210 WARNING: Could not fetch sub-slice from 1:909238-909238(1) on line 211 WARNING: Specified reference allele G does not match Ensembl reference allele on line 211 WARNING: Could not fetch sub-slice from 1:955597-955597(1) on line 212

ckandoth commented 8 years ago

Avoid specifying a different --ref-fasta. Let it use the GRCh37 fasta downloaded with VEP. Let me know what you find.

apastore commented 8 years ago

Not sure I have understand. My vcf is generated from bam align to hg19. Now I would like to annotate and convert to maf. Running previous version of vcf2maf I get a proper maf but not if I use the last version. Also I am not specifying any alternative ref-fasta and I am using the default one of vcf2maf.

Thanks Alessandro

ckandoth commented 8 years ago

Can you send me the exact command you used?

apastore commented 8 years ago

I do:

perl ~/sw/vcf2maf/vcf2maf.pl --input-vcf header.vcf \
--output-maf maf/${vcffile}.maf --maf-center . \
--tumor-id $Tumor --normal-id $Normal

and this is a sample vcf where I have the problem Thanks! Alessandro

fileformat=VCFv4.2

FILTER= 0.5 && (DP < 4 && %QUAL < 50))">

FILTER= 200.0">

FILTER= 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || HaplotypeScore > 13.0">

FILTER=

FILTER=

FILTER=

FILTER=

FILTER=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=

GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Sun Nov 01 12:11:52 EST 2015",Epoch=1446397912482,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_13_p1/chr1/1_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam, /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_blood/chr1/3_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar, NotPrimaryAlignment] disable_read_filter=[] intervals=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk-haplotype/chr1/13_13_p1-chr1_0_15687199-raw-regions-nolcr.bed] excludeIntervals=null interval_set_rule=INTERSECTION interval_merging=ALL interval_padding=0 reference_sequence=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=LENIENT_VCF_PROCESSING disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false out=/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk-haplotype/chr1/tx/tmpgMJ5t3/13_13_p1-chr1_0_15687199-raw.vcf.gz likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/variation/dbsnp_138.vcf.gz) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[BaseQualityRankSumTest, FisherStrand, GCContent, HaplotypeScore, HomopolymerRun, MappingQualityRankSumTest, MappingQualityZero, QualByDepth, ReadPosRankSumTest, RMSMappingQuality, DepthPerAlleleBySample, Coverage, ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.UnifiedGenotyper=<ID=UnifiedGenotyper,Version=3.4-46-gbc02625,Date="Sun Nov 01 20:47:18 EST 2015",Epoch=1446428838115,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_13_p1/chr1/1_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam, /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_blood/chr1/3_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar, NotPrimaryAlignment] disable_read_filter=[] intervals=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk/chr1/13_13_p1-chr1_0_15687199-raw-regions-nolcr.bed] excludeIntervals=null interval_set_rule=INTERSECTION interval_merging=ALL interval_padding=0 reference_sequence=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=LENIENT_VCF_PROCESSING disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false dbsnp=(RodBinding name=dbsnp source=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/variation/dbsnp_138.vcf.gz) comp=[] out=/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk/chr1/tx/tmp9c6qYA/13_13_p1-chr1_0_15687199-raw.vcf.gz onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[BaseQualityRankSumTest, FisherStrand, GCContent, HaplotypeScore, HomopolymerRun, MappingQualityRankSumTest, MappingQualityZero, QualByDepth, ReadPosRankSumTest, RMSMappingQuality, DepthPerAlleleBySample, Coverage] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine.VariantAnnotator=<ID=VariantAnnotator,Version=3.4-46-gbc02625,Date="Sun Nov 01 17:46:58 EST 2015",Epoch=1446418018125,CommandLineOptions="analysis_type=VariantAnnotator input_file=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_13_p1/chr1/1_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam, /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_blood/chr1/3_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar, NotPrimaryAlignment] disable_read_filter=[] intervals=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/varscan/chr1/13_13_p1-chr1_0_15687199-raw.vcf.gz] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=true useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=ALL disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/varscan/chr1/13_13_p1-chr1_0_15687199-raw.vcf.gz) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/variation/dbsnp_138.vcf.gz) comp=[] resource=[] out=/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/varscan/chr1/tx/tmpCDvfvP/13_13_p1-chr1_0_15687199-raw-gatkann.vcf.gz annotation=[BaseQualityRankSumTest, FisherStrand, GCContent, HaplotypeScore, HomopolymerRun, MappingQualityRankSumTest, MappingQualityZero, QualByDepth, ReadPosRankSumTest, RMSMappingQuality] excludeAnnotation=[] group=[] expression={} useAllAnnotations=false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine=<ID=MuTect,Version=2.7-1-g42d771f,Date="Sun Nov 01 09:45:10 EST 2015",Epoch=1446389110810,CommandLineOptions="analysis_type=MuTect input_file=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_13_p1/chr1/1_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam, /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_blood/chr1/3_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[NotPrimaryAlignment] intervals=[/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/mutect/chr1/13_13_p1-chr1_0_15687199-raw-mutect-regions.bed] excludeIntervals=null interval_set_rule=INTERSECTION interval_merging=ALL interval_padding=0 reference_sequence=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=ALLOW_N_CIGAR_READS disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false noop=false enable_extended_output=false enable_qscore_output=true artifact_detection_mode=false tumor_sample_name=s_13_13_p1 bam_tumor_sample_name=null normal_sample_name=s_13_blood force_output=false force_alleles=false only_passing_calls=false initial_tumor_lod=4.0 tumor_lod=6.3 fraction_contamination=0.02 minimum_mutation_cell_fraction=0.0 normal_lod=2.2 normal_artifact_lod=1.0 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 dbsnp_normal_lod=5.5 minimum_normal_allele_fraction=0.0 tumor_f_pretest=0.005 min_qscore=5 gap_events_threshold=3 heavily_clipped_read_fraction=0.3 fraction_mapq0_threshold=0.5 pir_median_threshold=10.0 pir_mad_threshold=3.0 required_maximum_alt_allele_mapping_quality_score=20 max_alt_alleles_in_normal_count=2 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 power_constant_af=0.30000001192092896 vcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub dbsnp=[(RodBinding name=dbsnp source=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/variation/dbsnp_138.vcf.gz)] cosmic=[(RodBinding name=cosmic source=/cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/variation/cosmic-v68-hg19.vcf.gz)] normal_panel=[] coverage_file=null coverage_20_q20_file=null power_file=null tumor_depth_file=null normal_depth_file=null filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

SnpEffCmd="SnpEff -formatEff -classic -cancer -i vcf -o vcf -s /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk/13_13_p1-effects-stats.html hg19 /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk/13_13_p1.vcf.gz "

SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani"

bcftools_filterCommand=filter -O v -T /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bedprep/AgilentExon_51MB_hg19_v3_targets.bed.gz --soft-filter GATKHardIndel -e 'QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0' -m + /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk/13_13_p1-effects-indel.vcf.gz

bcftools_filterVersion=1.2+htslib-1.2.1

bcftools_viewCommand=view -O z --exclude-types snps /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/gatk/13_13_p1-effects.vcf.gz

bcftools_viewVersion=1.2+htslib-1.2.1

commandline="/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/bin/freebayes -f /cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa --ploidy 2 --targets /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/freebayes/chr1/13_13_p1-chr1_0_15687199-raw-regions-nolcr.bed --min-repeat-entropy 1 --min-alternate-fraction 0.1 --pooled-discrete --pooled-continuous --genotype-qualities --report-genotype-likelihood-max --allele-balance-priors-off /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_13_p1/chr1/1_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/PCNSL/PCNSL/work/bamprep/s_13_blood/chr1/3_2015-10-05_PCNSL-sort.nsorted.disambiguatedSpeciesA.sorted-chr1_0_15687199-prep.bam"

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

contig=

fileDate=20151103

filter="QUAL > 5"

phasing=none

reference=file:///cbio/cslab/nobackup/pastore/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa

source=VarScan2

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_13_13_p1 s_13_blood

chr1 888639 rs3748596 T C 2772.20 PASS AC=4;AF=1;AN=4;DB;DP=200;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E306|749|NOC2L|protein_coding|CODING|NM_015658.3|9|C);FS=0;GC=61.35;HRun=1;HaplotypeScore=0;MLEAC=4;MLEAF=1;MQ=57.21;MQ0=0;QD=13.86;SOR=1.55 GT:AD:DP:GQ:PL 1/1:0,86:86:99:1685,123,0 1/1:0,113:114:81:1114,81,0 chr1 909238 rs3829740 G C 1817.20 PASS AC=4;AF=1;AN=4;DB;DP=162;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R487P|611|PLEKHN1|protein_coding|CODING|NM_032129.2|14|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGt/cCt|R452P|576|PLEKHN1|protein_coding|CODING|NM_001160184.1|13|C),DOWNSTREAM(MODIFIER||1341||790|PERM1|protein_coding|CODING|NM_001291366.1||C),DOWNSTREAM(MODIFIER||1341||696|PERM1|protein_coding|CODING|NM_001291367.1||C);FS=0;GC=67.58;HRun=1;HaplotypeScore=0.9665;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=11.22;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,48:48:75:1019,75,0 1/1:1,113:114:60:825,60,0 chr1 955597 rs115173026 G T 90.28 PASS AC=2;AF=1;AN=2;DB;DP=10;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P15|2045|AGRN|protein_coding|CODING|NM_198576.3|1|T);FS=0;GC=79.8;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=9.03;SOR=2.833 GT:AD:DP:GQ:PL 1/1:3,7:10:9:118,9,0 ./.:.:.:.:. chr1 3379659 . G A 405.44 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=1.096;DP=82;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R4Q|709|ARHGEF16|protein_coding|CODING|NM_014448.3|2|A);FS=15.315;GC=69.08;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=-0.745;QD=8.81;ReadPosRankSum=-0.921;SOR=1.391 GT:AD:DP:GQ:PL 0/1:24,22:46:99:434,0,106 0/0:36,0:36:6:0,6,82 chr1 3416449 rs7553399 C A 290.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.362;DB;DP=53;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cTg|R916L|1541|MEGF6|protein_coding|CODING|NM_001409.3|22|A);FS=10.296;GC=67.83;HRun=0;HaplotypeScore=0.4998;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.725;QD=5.48;ReadPosRankSum=0.181;SOR=0.32 GT:AD:DP:GQ:PL 0/1:16,19:35:99:285,0,192 0/1:10,7:18:34:34,0,36 chr1 3418391 rs4648508 C T . PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-3.187;DB;DP=32;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P761|1541|MEGF6|protein_coding|CODING|NM_001409.3|18|T);FS=74.361;GC=73.27;GPV=1;HRun=0;MQ=60;MQ0=0;MQRankSum=0.166;ReadPosRankSum=1.824;SOMATIC;SPV=0.0071858;SS=2;SSC=21 GT:AD:DP:DP4:FREQ:RD 0/1:13:24:11,0,5,8:0.5417:11 0/0:0:8:8,0,0,0:0:8 chr1 3638674 rs1801174 C T 2070.20 PASS AC=4;AF=1;AN=4;DB;DP=181;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|636|TP73|protein_coding|CODING|NM_005427.3|5|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|499|TP73|protein_coding|CODING|NM_001204184.1|5|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|475|TP73|protein_coding|CODING|NM_001204185.1|5|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|403|TP73|protein_coding|CODING|NM_001204186.1|5|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|555|TP73|protein_coding|CODING|NM_001204187.1|5|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T173|540|TP73|protein_coding|CODING|NM_001204188.1|5|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T124|587|TP73|protein_coding|CODING|NM_001126240.2|3|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T124|450|TP73|protein_coding|CODING|NM_001126241.2|3|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T124|426|TP73|protein_coding|CODING|NM_001126242.2|3|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T124|354|TP73|protein_coding|CODING|NM_001204189.1|3|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T124|506|TP73|protein_coding|CODING|NM_001204190.1|3|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T124|491|TP73|protein_coding|CODING|NM_001204191.1|3|T),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T102|565|TP73|protein_coding|CODING|NM_001204192.1|3|T);FS=0;GC=64.59;HRun=0;HaplotypeScore=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=11.44;SOR=1.292 GT:AD:DP:GQ:PL 1/1:0,73:73:99:1509,111,0 1/1:0,107:108:45:588,45,0 chr1 9324213 rs17368528 C T 922.45 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.135;DB;DP=127;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P565L|802|H6PD|protein_coding|CODING|NM_001282587.1|5|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P554L|791|H6PD|protein_coding|CODING|NM_004285.3|5|T);FS=14.235;GC=65.84;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.182;QD=7.26;ReadPosRankSum=0.826;SOR=0.02 GT:AD:DP:GQ:PL 0/1:36,47:83:99:926,0,245 0/1:31,13:44:25:25,0,145 chr1 9670834 rs4926472 C T 497.77 PASS AC=2;AF=1;AN=2;DB;DP=36;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCg/cTg|P579L|666|TMEM201|protein_coding|CODING|NM_001130924.2|9|T);FS=0;GC=68.08;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=17.16;SOR=2.985 GT:AD:DP:GQ:PL 1/1:0,29:29:39:526,39,0 ./.:.:.:.:. chr1 9932090 rs139825449 C T 953.45 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.542;DB;DP=106;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P11|81|CTNNBIP1|protein_coding|CODING|NM_001012329.1|3|T),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P11|81|CTNNBIP1|protein_coding|CODING|NM_020248.2|4|T);FS=24.228;GC=63.84;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.011;QD=8.99;ReadPosRankSum=0.498;SOR=0.009 GT:AD:DP:GQ:PL 0/1:33,45:78:99:959,0,352 0/1:16,12:28:23:23,0,185 chr1 10435324 rs11121552 C A 326.54 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-0.116;DB;DP=105;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acA|T1721|1770|KIF1B|protein_coding|CODING|NM_015074.3|46|A);FS=18.145;GC=45.39;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=0.615;QD=5.18;ReadPosRankSum=0.947;SOR=4.407 GT:AD:DP:GQ:PL 0/1:25,38:63:99:356,0,655 0/0:24,18:42:12:0,12,163 chr1 11579504 rs2072993 G C 947.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-0.25;DB;DP=119;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGc/gCc|G661A|1392|PTCHD2|protein_coding|CODING|NM_020780.1|8|C);FS=2.289;GC=63.09;HRun=4;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.45;QD=7.96;ReadPosRankSum=1.399;SOR=1.071 GT:AD:DP:GQ:PL 0/1:35,44:79:99:873,0,609 0/1:19,21:40:99:103,0,142 chr1 11839972 rs41275462 G A 340.41 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=0.794;DB;DP=38;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R922Q|1449|C1orf167|protein_coding|CODING|NM_001010881.1|13|A);FS=0;GC=66.58;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=-0.794;QD=14.18;ReadPosRankSum=-0.938;SOR=0.33 GT:AD:DP:GQ:PL 0/1:8,16:24:39:368,0,39 0/0:7,7:14:3:0,3,41 chr1 11844330 rs10864543 C T 427.54 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=2.115;DB;DP=79;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1035|1449|C1orf167|protein_coding|CODING|NM_001010881.1|15|T),DOWNSTREAM(MODIFIER||1457||656|MTHFR|protein_coding|CODING|NM_005957.4||T);FS=34.561;GC=63.09;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=-0.581;QD=8.38;ReadPosRankSum=1.327;SOR=0.715 GT:AD:DP:GQ:PL 0/1:30,21:51:99:457,0,357 0/0:15,13:28:12:0,12,161 chr1 12082926 rs2295283 A G 1061.21 PASS AC=4;AF=1;AN=4;DB;DP=89;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Gag|K167E|388|MIIP|protein_coding|CODING|NM_021933.3|4|G);FS=0;GC=57.86;HRun=0;HaplotypeScore=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=11.92;SOR=3.098 GT:AD:DP:GQ:PL 1/1:0,40:40:54:750,54,0 1/1:0,49:49:24:338,24,0 chr1 15754484 rs2473356 T C 2399.20 PASS AC=4;AF=1;AN=4;DB;DP=118;Dels=0;EFF=INTRON(MODIFIER||||240|EFHD2|protein_coding|CODING|NM_024329.5|3|C);FS=0;GC=54.61;HRun=0;HaplotypeScore=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=20.33;SOR=0.99 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2001,141,0 1/1:0,47:48:30:425,30,0 chr1 17296882 rs41303881 G A 203.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-2.144;DB;DP=101;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R1862|2017|CROCC|protein_coding|CODING|NM_014675.4|34|A),DOWNSTREAM(MODIFIER||4117||183|MFAP2|protein_coding|CODING|NM_002403.3||A),DOWNSTREAM(MODIFIER||4117||182|MFAP2|protein_coding|CODING|NM_001135248.1||A),DOWNSTREAM(MODIFIER||4117||182|MFAP2|protein_coding|CODING|NM_001135247.1||A),DOWNSTREAM(MODIFIER||4117||183|MFAP2|protein_coding|CODING|NM_017459.2||A);FS=11.695;GC=64.59;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.158;QD=2.01;ReadPosRankSum=0.519;SOR=3.611 GT:AD:DP:GQ:PL 0/1:21,22:43:99:188,0,362 0/1:25,33:58:44:44,0,335 chr1 17313343 rs9435659 G A 279.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=0.722;DB;DP=65;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1064|1180|ATP13A2|protein_coding|CODING|NM_022089.3|27|A),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1059|1175|ATP13A2|protein_coding|CODING|NM_001141973.2|27|A),SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1020|1158|ATP13A2|protein_coding|CODING|NM_001141974.2|26|A);FS=14.548;GC=66.58;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.394;QD=4.3;ReadPosRankSum=1.116;SOR=0.009 GT:AD:DP:GQ:PL 0/1:22,16:38:99:280,0,266 0/1:12,15:27:28:28,0,110 chr1 17657534 rs11203366 G A 2774.20 PASS AC=4;AF=1;AN=4;DB;DP=253;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G55S|663|PADI4|protein_coding|CODING|NM_012387.2|2|A);FS=0;GC=58.1;HRun=0;HaplotypeScore=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=10.97;SOR=1.051 GT:AD:DP:GQ:PL 1/1:0,88:88:99:2093,157,0 1/1:0,165:165:54:708,54,0 chr1 19408294 rs67232976 G GC 4842.15 PASS AC=3;AF=0.75;AN=4;BaseQRankSum=3.579;DB;DP=293;EFF=INTRON(MODIFIER||||5183|UBR4|protein_coding|CODING|NM_020765.2|102|GC);FS=12.18;GC=51.12;HRun=0;MLEAC=3;MLEAF=0.75;MQ=60.37;MQ0=0;MQRankSum=-0.732;QD=16.53;RPA=4,5;RU=C;ReadPosRankSum=-2.373;SOR=1.013;STR GT:AD:DP:GQ:PL 1/1:14,100:143:48:3470,48,0 0/1:30,66:150:99:1411,0,202 chr1 20141283 rs1541184 C T 1037.44 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=1.563;DB;DP=163;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A104|227|RNF186|protein_coding|CODING|NM_019062.1|1|T);FS=28.542;GC=65.59;HRun=0;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=0.468;QD=6.36;ReadPosRankSum=1.244;SOR=0.005 GT:AD:DP:GQ:PL 0/1:53,58:111:99:1033,0,420 0/1:25,27:52:33:33,0,35 chr1 20987873 rs537816 G C 2390.77 PASS AC=2;AF=1;AN=2;DB;DP=127;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Ggt|R8G|456|DDOST|protein_coding|CODING|NM_005216.4|1|C),DOWNSTREAM(MODIFIER||2634||1029|KIF17|protein_coding|CODING|NM_020816.3||C),DOWNSTREAM(MODIFIER||2634||1028|KIF17|protein_coding|CODING|NM_001122819.2||C),DOWNSTREAM(MODIFIER||2634||929|KIF17|protein_coding|CODING|NM_001287212.1||C);FS=0;GC=64.84;HRun=1;HaplotypeScore=0;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;QD=20.09;SOR=0.917 GT:AD:DP:GQ:PL 1/1:0,119:119:99:2419,178,0 ./.:.:.:.:. chr1 21806710 rs12034222 T G 97.44 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=2.807;DB;DP=41;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L459V|633|NBPF3|protein_coding|CODING|NM_032264.4|11|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L447V|621|NBPF3|protein_coding|CODING|NM_001256416.2|11|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L389V|563|NBPF3|protein_coding|CODING|NM_001256417.2|10|G),EXON(MODIFIER|||||NBPF3||CODING|NR_046176.2|14|G);FS=28.543;GC=47.63;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=44.72;MQ0=1;MQRankSum=-1.893;QD=3.75;ReadPosRankSum=0.196;SOR=3.219 GT:AD:DP:GQ:PL 0/1:22,4:26:99:126,0,305 0/0:15,0:15:6:0,6,71 chr1 24134721 rs719400 T C 1379.71 PASS AC=4;AF=1;AN=4;DB;DP=53;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L218|325|HMGCL|protein_coding|CODING|NM_000191.2|7|C),SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L147|254|HMGCL|protein_coding|CODING|NM_001166059.1|5|C);FS=0;GC=53.37;HRun=0;HaplotypeScore=0;MLEAC=4;MLEAF=1;MQ=60;MQ0=0;QD=26.03;SOR=2.774 GT:AD:DP:GQ:PL 1/1:0,41:41:93:1322,93,0 1/1:0,12:12:6:84,6,0 chr1 24201109 rs2229580 C T 467.47 PASS AC=2;AF=0.5;AN=4;BaseQRankSum=-3.171;DB;DP=128;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P333|360|CNR2|protein_coding|CODING|NM_001841.2|2|T);FS=50.655;GC=52.87;HRun=1;HaplotypeScore=0;MLEAC=2;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.858;QD=3.65;ReadPosRankSum=1.753;SOR=5.416 GT:AD:DP:GQ:PL 0/1:30,40:70:38:476,0,38 0/1:29,29:58:20:20,0,191 chr1 24447942 . C T 251.54 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-1.682;DP=64;Dels=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G360R|574|IL22RA1|protein_coding|CODING|NM_021258.3|7|T);FS=3.31;GC=60.85;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=-0.872;QD=5.99;ReadPosRankSum=1.927;SOR=0.082 GT:AD:DP:GQ:PL 0/1:20,22:42:86:281,0,86 0/0:22,0:22:12:0,12,162 chr1 24859617 rs196429 G A 302.62 PASS AC=1;AF=0.25;AN=4;BaseQRankSum=-0.589;DB;DP=61;Dels=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P138|241|RCAN3|protein_coding|CODING|NM_001251977.1|4|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P138|241|RCAN3|protein_coding|CODING|NM_001251979.1|4|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P13|116|RCAN3|protein_coding|CODING|NM_001251984.1|3|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P80|183|RCAN3|protein_coding|CODING|NM_001251981.1|3|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P13|116|RCAN3|protein_coding|CODING|NM_001251983.1|3|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P138|241|RCAN3|protein_coding|CODING|NM_013441.3|4|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P138|241|RCAN3|protein_coding|CODING|NM_001251978.1|4|A),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P128|231|RCAN3|protein_coding|CODING|NM_001251980.1|3|A),INTRON(MODIFIER||||173|RCAN3|protein_coding|CODING|NM_001251982.1|2|A),INTRON(MODIFIER||||115|RCAN3|protein_coding|CODING|NM_001251985.1|1|A);FS=6.99;GC=43.64;HRun=0;HaplotypeScore=0;MLEAC=1;MLEAF=0.25;MQ=60;MQ0=0;MQRankSum=-0.589;QD=10.09;ReadPosRankSum=0.118;SOR=3.014 GT:AD:DP:GQ:PL 0/1:12,18:30:10:330,0,10 0/0:17,14:31:3:0,3,42

On Nov 5, 2015, at 8:20 AM, Cyriac Kandoth notifications@github.com wrote:

Can you send me the exact command you used?

— Reply to this email directly or view it on GitHub https://github.com/mskcc/vcf2maf/issues/29#issuecomment-154057541.

ckandoth commented 8 years ago

Hi Alessandro. Sorry for putting this on the backburner. It looks like the latest version of VEP will not natively handle the chr-prefixes that hg19 uses. But it will respect a custom reference that you define. So the only thing you need to do is specify the hg19 fasta using vcf2maf --ref-fasta. Let me know if that works, and I will close out this issue.

apastore commented 8 years ago

Ok I will try, but I have already try the old maf2vcf with VEP82 and it work fine also with the chr string

On Nov 23, 2015, at 3:08 PM, Cyriac Kandoth notifications@github.com wrote:

Hi Alessandro. Sorry for putting this on the backburner. It looks like the latest version of VEP will not natively handle the chr-prefixes that hg19 uses. But it will respect a custom reference that you define. So the only thing you need to do is specify the hg19 fasta using vcf2maf --ref-fasta. Let me know if that works, and I will close out this issue.

— Reply to this email directly or view it on GitHub https://github.com/mskcc/vcf2maf/issues/29#issuecomment-159048755.

ckandoth commented 8 years ago

Ok thanks. The old maf2vcf or maf2maf should also have worked fine, because it forced a conversion from hg19 to GRCh37. But the latest version is truly agnostic of reference genome. So you'll need to specify --ref-fasta to get it to work correctly. I'll close this issue, but feel free to reopen if you find a related bug.

sgosline commented 8 years ago

I found this issue via google, and wanted to add that if you provide the hg19.fasta file, VEP still provides warnings in cases where the fasta file is in lower case: e.g. "Specified reference allele G does not match Ensembl reference allele g"

This was fixed by changing a line in line 3192 of /Bio/EnsEMBL/Variation/Utils/VEP.pm where I added an 'lc' to the 'eq' function.

apastore commented 8 years ago

Thanks for you advice! Alessandro

On Dec 7, 2015, at 4:15 PM, Sara JC Gosline notifications@github.com wrote:

I found this issue via google, and wanted to add that if you provide the hg19.fasta file, VEP still provides warnings in cases where the fasta file is in lower case: e.g. "Specified reference allele G does not match Ensembl reference allele g"

This was fixed by changing a line in line 3192 of /Bio/EnsEMBL/Variation/Utils/VEP.pm where I added an 'lc' to the 'eq' function.

— Reply to this email directly or view it on GitHub https://github.com/mskcc/vcf2maf/issues/29#issuecomment-162665723.