Error with VEP annotation in updated development version.

[PatrickJReed]

I updated bcbio to use the more robust dbNSFP VEP annotation and am getting an error I haven't seen before.

[2017-02-06T18:02Z] Ensemble consensus calls for Kindred_87: samtools,platypus,gatk-haplotype,freebayes,varscan [2017-02-06T18:02Z] Ensemble intersection calling: Kindred_87 [2017-02-06T18:32Z] 2017-02-06 18:32:08 ip-172-31-21-143.us-west-2.compute.internal INFO [bcbio.run.itx] - Note: -w option not given, printing list of sites... [2017-02-06T18:36Z] 2017-02-06 18:36:00 ip-172-31-21-143.us-west-2.compute.internal ERROR [bcbio.variation.recall.main] - [2017-02-06T18:36Z] htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 882: The VCF specification does not allow for whitespace in the INFO field. Offending field value was "AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T

.......

for input source: /efs/Kindred87/work/bcbiotx/tmpIbN3NQ/Kindred_87-ensemble-work/Kindred_87-samtools-nofilter.vcf.gz [2017-02-06T18:36Z] htsjdk.variant.vcf.AbstractVCFCodec.generateException AbstractVCFCodec.java: 780 [2017-02-06T18:36Z] htsjdk.variant.vcf.AbstractVCFCodec.parseInfo AbstractVCFCodec.java: 406 [2017-02-06T18:36Z] htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine AbstractVCFCodec.java: 321 [2017-02-06T18:36Z] htsjdk.variant.vcf.AbstractVCFCodec.decodeLine AbstractVCFCodec.java: 279 [2017-02-06T18:36Z] htsjdk.variant.vcf.AbstractVCFCodec.decode AbstractVCFCodec.java: 257 [2017-02-06T18:36Z] htsjdk.variant.vcf.AbstractVCFCodec.decode AbstractVCFCodec.java: 60 [2017-02-06T18:36Z] htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord TabixFeatureReader.java: 165 [2017-02-06T18:36Z] htsjdk.tribble.TabixFeatureReader$FeatureIterator. TabixFeatureReader.java: 150 [2017-02-06T18:36Z] htsjdk.tribble.TabixFeatureReader.query TabixFeatureReader.java: 125 [2017-02-06T18:36Z] sun.reflect.GeneratedMethodAccessor6.invoke :
[2017-02-06T18:36Z] sun.reflect.DelegatingMethodAccessorImpl.invoke DelegatingMethodAccessorImpl.java: 43 [2017-02-06T18:36Z] java.lang.reflect.Method.invoke Method.java: 498 [2017-02-06T18:36Z] clojure.lang.Reflector.invokeMatchingMethod Reflector.java: 93 [2017-02-06T18:36Z] clojure.lang.Reflector.invokeInstanceMethod Reflector.java: 28 [2017-02-06T18:36Z] bcbio.variation.variantcontext/variants-in-region/get-vcs-in-source variantcontext.clj: 110 [2017-02-06T18:36Z] clojure.core/map/fn core.clj: 2624 [2017-02-06T18:36Z] clojure.lang.LazySeq.sval LazySeq.java: 40 [2017-02-06T18:36Z] clojure.lang.LazySeq.seq LazySeq.java: 49 [2017-02-06T18:36Z] clojure.lang.RT.seq RT.java: 507 [2017-02-06T18:36Z] clojure.core/seq core.clj: 137 [2017-02-06T18:36Z] clojure.core/apply core.clj: 630 [2017-02-06T18:36Z] clojure.core/mapcat core.clj: 2660 [2017-02-06T18:36Z] clojure.lang.RestFn.invoke RestFn.java: 423 [2017-02-06T18:36Z] bcbio.variation.variantcontext/variants-in-region variantcontext.clj: 112 [2017-02-06T18:36Z] bcbio.variation.variantcontext/variants-in-region variantcontext.clj: 107 [2017-02-06T18:36Z] bcbio.variation.ensemble.intersect/get-rep-vc/fn intersect.clj: 50 [2017-02-06T18:36Z] clojure.core/comp/fn core.clj: 2438 [2017-02-06T18:36Z] clojure.core/map/fn core.clj: 2624 [2017-02-06T18:36Z] clojure.lang.LazySeq.sval LazySeq.java: 40 [2017-02-06T18:36Z] clojure.lang.LazySeq.seq LazySeq.java: 49 [2017-02-06T18:36Z] clojure.lang.RT.seq RT.java: 507 [2017-02-06T18:36Z] clojure.core/seq core.clj: 137 [2017-02-06T18:36Z] clojure.core/map/fn core.clj: 2616 ' returned non-zero exit status 1

Basics of my config:

details:

• algorithm: adapters:
  • truseq
  • illumina align_split_size: 5000000 aligner: bwa effects: vep ensemble: numpass: 2 mark_duplicates: true phasing: false quality_format: illumina realign: false recalibrate: false remove_lcr: true tools_off:
  • gemini tools_on:
  • bwa-mem
  • gemini_vcfanno
  • qualimap variantcaller:
  • samtools
  • platypus
  • gatk-haplotype
  • freebayes
  • varscan analysis: variant2 description: 2011-925 files:
  • /efs/K87/2011-925_110823_SN484_0112_AC029KACXX_2_1_sequence.txt.gz
  • /efs/K87/2011-925_110823_SN484_0112_AC029KACXX_2_2_sequence.txt.gz genome_build: GRCh37 metadata: batch: Kindred_87 description: null phenotype: null

[chapmanb]

Patrick -- thanks for the report. The recent VEP changes added a lot of new fields from dbNSFP and it looks like one of them may be invalid. Would it be possible to find the offending line listed in the error message:

zgrep 'AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487' /efs/Kindred87/work/bcbiotx/tmpIbN3NQ/Kindred_87-ensemble-work/Kindred_87-samtools-nofilter.vcf.gz

and post it here so we can identify the problem one and remove it. @matthdsm -- do you think we could trim the list of dbNSFP fields in any way?

[PatrickJReed]

I went to pull out the referenced line but the bcbiotx folder is empty? Here is the complete description of the offending field value from the log.

[2017-02-07T03:59Z] Ensemble consensus calls for Kindred_87: samtools,platypus,gatk-haplotype,freebayes,varscan [2017-02-07T04:27Z] Uncaught exception occurred Traceback (most recent call last): File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run _do_run(cmd, checks, log_stdout, env=env) File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 102, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && /usr/local/share/bcbio/anaconda/bin/bcbio-variation-recall ensemble --cores=16 --numpass 2 --names samtools,platypus,gatk-haplotype,freebayes,varscan --nofiltered /efs/Kindred87/work/bcbiotx/tmp7jc1CM/Kindred_87-ensemble.vcf.gz /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa /efs/Kindred87/work/gemini/Kindred_87-samtools.vcf.gz /efs/Kindred87/work/gemini/Kindred_87-platypus.vcf.gz /efs/Kindred87/work/gemini/Kindred_87-gatk-haplotype.vcf.gz /efs/Kindred87/work/gemini/Kindred_87-freebayes.vcf.gz /efs/Kindred87/work/gemini/Kindred_87-varscan.vcf.gz 2017-02-07 04:23:30 ip-172-31-21-143.us-west-2.compute.internal INFO [bcbio.run.itx] - Note: -w option not given, printing list of sites... 2017-02-07 04:27:26 ip-172-31-21-143.us-west-2.compute.internal ERROR [bcbio.variation.recall.main] - htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 882: The VCF specification does not allow for whitespace in the INFO field. Offending field value was "AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|||||-/2790|-/2250|-/749|||COSM5053725|288|-1||SNV|HGNC|24517|YES|||CCDS3.1|ENSP00000317992|Q9Y3T9||UPI000041820C|1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding|12/12||ENST00000341065.4:c.1532G>T|ENSP00000349216.4:p.Arg511Ser|1532/2191|1533/1770|511/589|R/S|agG/agT|COSM5053725||1|cds_start_NF|SNV|HGNC|28706|||||ENSP00000349216|||UPI000155D47A||deleterious(0)|benign(0.041)|Gene3D:1.10.150.50&hmmpanther:PTHR12247&hmmpanther:PTHR12247:SF67&SMART_domains:SM00454||||||||||||||||||||1|1||||||23.3|3.735147|0.50581|0.45464|0.98767157234535885|2.931379|0.146056818176487|0.47322|2.813854|0.0814994945588303|c||||5.43|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|T|0.40875|0.0185926580766|T|0.37511|0.1012|T|0.40788|-0.9512|SAM11_HUMAN|M|2.63|0.77240|R603S|R603S|0.28656|simple_aae|N|0.837155|0.65929|D&.&.&.&.&.|-3.31&.&.&.&.&.|9|7.5435|0.26756|0.1474:0.0:0.7184:0.1342|ENST00000455979&ENST00000342066&CCDS2.2&ENST00000341065&NM_152486.2|R462S&R603S&R603S&R510S&R603S|0.54289|0.497&0.288&0.133&0.456&0.288|||||AEFBHCI|D|0.37829|0.77508|0|0.403107|0.05239|1.000000|0.71511|0.993000|0.57359|2.102000|0.41182|1.045000|0.66922||||,T|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|14/14||ENST00000342066.3:c.1809G>T|ENSP00000342313.3:p.Arg603Ser|1892/2551|1809/2046|603/681|R/S|agG/agT|COSM5053725||1||SNV|HGNC|28706|YES|||CCDS2.2|ENSP00000342313|Q96NU1|Q5SV95&I7FV93&A6PWC8|UPI0000D61E04||deleterious(0.02)|benign(0.232)|Gene3D:1.10.150.50&hmmpanther:PTHR12247&hmmpanther:PTHR12247:SF67&SMART_domains:SM00454||||||||||||||||||||1|1||||||23.3|3.735147|0.50581|0.45464|0.98767157234535885|2.931379|0.146056818176487|0.47322|2.813854|0.0814994945588303|c||||5.43|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|T|0.40875|0.0185926580766|T|0.37511|0.1012|T|0.40788|-0.9512|SAM11_HUMAN|M|2.63|0.77240|R603S|R603S|0.28656|simple_aae|N|0.837155|0.65929|D&.&.&.&.&.|-3.31&.&.&.&.&.|9|7.5435|0.26756|0.1474:0.0:0.7184:0.1342|ENST00000455979&ENST00000342066&CCDS2.2&ENST00000341065&NM_152486.2|R462S&R603S&R603S&R510S&R603S|0.54289|0.497&0.288&0.133&0.456&0.288|||||AEFBHCI|D|0.37829|0.77508|0|0.403107|0.05239|1.000000|0.71511|0.993000|0.57359|2.102000|0.41182|1.045000|0.66922||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000420190|protein_coding|||||-/626|-/537|-/179|||COSM5053725|4625|1|cds_end_NF|SNV|HGNC|28706|||||ENSP00000411579||Q5SV95&I7FV93&A6PWC8|UPI000155D47C||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding|7/7||ENST00000455979.1:c.1388G>T|ENSP00000412228.1:p.Arg463Ser|1388/1731|1389/1626|463/541|R/S|agG/agT|COSM5053725||1|cds_start_NF|SNV|HGNC|28706|||||ENSP00000412228|||UPI000155D479||deleterious(0)|benign(0.236)|||||||||||||||||||||1|1||||||23.3|3.735147|0.50581|0.45464|0.98767157234535885|2.931379|0.146056818176487|0.47322|2.813854|0.0814994945588303|c||||5.43|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|T|0.40875|0.0185926580766|T|0.37511|0.1012|T|0.40788|-0.9512|SAM11_HUMAN|M|2.63|0.77240|R603S|R603S|0.28656|simple_aae|N|0.837155|0.65929|D&.&.&.&.&.|-3.31&.&.&.&.&.|9|7.5435|0.26756|0.1474:0.0:0.7184:0.1342|ENST00000455979&ENST00000342066&CCDS2.2&ENST00000341065&NM_152486.2|R462S&R603S&R603S&R510S&R603S|0.54289|0.497&0.288&0.133&0.456&0.288|||||AEFBHCI|D|0.37829|0.77508|0|0.403107|0.05239|1.000000|0.71511|0.993000|0.57359|2.102000|0.41182|1.045000|0.66922||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron|||||-/657|||||COSM5053725|1024|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron|||||-/542|||||COSM5053725|1114|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron|||||-/862|||||COSM5053725|922|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|||||-/4201|||||COSM5053725|289|-1||SNV|HGNC|24517|||||||||1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript|||||-/318|||||COSM5053725|1743|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron|||||-/1611|||||COSM5053725|288|-1||SNV|HGNC|24517|||||||||1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript|||||-/149|||||COSM5053725|1403|-1||SNV|HGNC|24517|||||||||1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000341968|promoter_flanking_region||||||||||COSM5053725||||SNV||||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000341969|CTCF_binding_site||||||||||COSM5053725||||SNV||||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||", for input source: /efs/Kindred87/work/bcbiotx/tmp7jc1CM/Kindred_87-ensemble-work/Kindred_87-samtools-nofilter.vcf.gz htsjdk.variant.vcf.AbstractVCFCodec.generateException AbstractVCFCodec.java: 780 htsjdk.variant.vcf.AbstractVCFCodec.parseInfo AbstractVCFCodec.java: 406 htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine AbstractVCFCodec.java: 321 htsjdk.variant.vcf.AbstractVCFCodec.decodeLine AbstractVCFCodec.java: 279 htsjdk.variant.vcf.AbstractVCFCodec.decode AbstractVCFCodec.java: 257 htsjdk.variant.vcf.AbstractVCFCodec.decode AbstractVCFCodec.java: 60 htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord TabixFeatureReader.java: 165 htsjdk.tribble.TabixFeatureReader$FeatureIterator. TabixFeatureReader.java: 150 htsjdk.tribble.TabixFeatureReader.query TabixFeatureReader.java: 125 sun.reflect.GeneratedMethodAccessor6.invoke :
sun.reflect.DelegatingMethodAccessorImpl.invoke DelegatingMethodAccessorImpl.java: 43 java.lang.reflect.Method.invoke Method.java: 498 clojure.lang.Reflector.invokeMatchingMethod Reflector.java: 93 clojure.lang.Reflector.invokeInstanceMethod Reflector.java: 28 bcbio.variation.variantcontext/variants-in-region/get-vcs-in-source variantcontext.clj: 110 clojure.core/map/fn core.clj: 2624 clojure.lang.LazySeq.sval LazySeq.java: 40 clojure.lang.LazySeq.seq LazySeq.java: 49 clojure.lang.RT.seq RT.java: 507 clojure.core/seq core.clj: 137 clojure.core/apply core.clj: 630 clojure.core/mapcat core.clj: 2660 clojure.lang.RestFn.invoke RestFn.java: 423 bcbio.variation.variantcontext/variants-in-region variantcontext.clj: 112 bcbio.variation.variantcontext/variants-in-region variantcontext.clj: 107 bcbio.variation.ensemble.intersect/get-rep-vc/fn intersect.clj: 50 clojure.core/comp/fn core.clj: 2438 clojure.core/map/fn core.clj: 2624 clojure.lang.LazySeq.sval LazySeq.java: 40 clojure.lang.LazySeq.seq LazySeq.java: 49 clojure.lang.RT.seq RT.java: 507 clojure.core/seq core.clj: 137 clojure.core/map/fn core.clj: 2616 clojure.lang.LazySeq.sval LazySeq.java: 40 clojure.lang.LazySeq.seq LazySeq.java: 49 clojure.lang.Cons.next Cons.java: 39 clojure.lang.RT.next RT.java: 674 clojure.core/next core.clj: 64 bcbio.variation.variantcontext/write-vcf-w-template variantcontext.clj: 189 clojure.lang.RestFn.invoke RestFn.java: 573 bcbio.variation.ensemble.intersect/ensemble-vcfs/fn intersect.clj: 88 bcbio.variation.ensemble.intersect/ensemble-vcfs intersect.clj: 86 bcbio.variation.ensemble.intersect/-main intersect.clj: 140 clojure.lang.RestFn.applyTo RestFn.java: 137 clojure.core/apply core.clj: 630 bcbio.variation.recall.main/-main/fn main.clj: 34 bcbio.variation.recall.main/-main main.clj: 33 clojure.lang.RestFn.applyTo RestFn.java: 137 bcbio.variation.recall.main.main :

' returned non-zero exit status 1

I can grep the matching lines from the vcfs in work/samtools if it would help. Kindred_87.vcf.gz
Kindred_87-vepeffects-filter.vcf.gz Kindred_87-vepeffects.vcf.gz

[matthdsm]

Hi Brad, Patrick.

This is an issue I haven't encountered before. As far as I know, the dbNSFP field names contain no whitespaces. That being said, the dbNSFP file gets modified quite a bit to be useful for GRCh37. @chapmanb do you think this could be the issue? @PatrickJReed, is it possible for you to test the same config on hg38?

I do notice a field with whitespace in the CSQ field on the offending line:

|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|

But that kind of values hasn't stopped any of my tests before. Sorry I can't be of much help. M

[chapmanb]

Patrick and Matthias; Thanks for helping to debug this. I agree that it's like whitespace in the Sterile alpha motif description. We'll have to figure out what field this is and exclude it, but it's a bit tricky because of the large number of annotations. Would it be possible to get the header and the problem line:

zgrep '##INFO=<ID=CSQ` Kindred_87-vepeffects.vcf.gz
zgrep 'AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487' Kindred_87-vepeffects.vcf.gz

Thanks again.

[PatrickJReed]

zgrep '##INFO=<ID=CSQ' Kindred_87-vepeffects.vcf.gz

INFO=

zgrep 'AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487' Kindred_87-vepeffects.vcf.gz 1 879296 . G T 17.75 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|||||-/2790|-/2250|-/749|||COSM5053725|288|-1||SNV|HGNC|24517|YES|||CCDS3.1|ENSP00000317992|Q9Y3T9||UPI000041820C|1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding|12/12||ENST00000341065.4:c.1532G>T|ENSP00000349216.4:p.Arg511Ser|1532/2191|1533/1770|511/589|R/S|agG/agT|COSM5053725||1|cds_start_NF|SNV|HGNC|28706|||||ENSP00000349216|||UPI000155D47A||deleterious(0)|benign(0.041)|Gene3D:1.10.150.50&hmmpanther:PTHR12247&hmmpanther:PTHR12247:SF67&SMART_domains:SM00454||||||||||||||||||||1|1||||||23.3|3.735147|0.50581|0.45464|0.98767157234535885|2.931379|0.146056818176487|0.47322|2.813854|0.0814994945588303|c||||5.43|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|T|0.40875|0.0185926580766|T|0.37511|0.1012|T|0.40788|-0.9512|SAM11_HUMAN|M|2.63|0.77240|R603S|R603S|0.28656|simple_aae|N|0.837155|0.65929|D&.&.&.&.&.|-3.31&.&.&.&.&.|9|7.5435|0.26756|0.1474:0.0:0.7184:0.1342|ENST00000455979&ENST00000342066&CCDS2.2&ENST00000341065&NM_152486.2|R462S&R603S&R603S&R510S&R603S|0.54289|0.497&0.288&0.133&0.456&0.288|||||AEFBHCI|D|0.37829|0.77508|0|0.403107|0.05239|1.000000|0.71511|0.993000|0.57359|2.102000|0.41182|1.045000|0.66922||||,T|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|14/14||ENST00000342066.3:c.1809G>T|ENSP00000342313.3:p.Arg603Ser|1892/2551|1809/2046|603/681|R/S|agG/agT|COSM5053725||1||SNV|HGNC|28706|YES|||CCDS2.2|ENSP00000342313|Q96NU1|Q5SV95&I7FV93&A6PWC8|UPI0000D61E04||deleterious(0.02)|benign(0.232)|Gene3D:1.10.150.50&hmmpanther:PTHR12247&hmmpanther:PTHR12247:SF67&SMART_domains:SM00454||||||||||||||||||||1|1||||||23.3|3.735147|0.50581|0.45464|0.98767157234535885|2.931379|0.146056818176487|0.47322|2.813854|0.0814994945588303|c||||5.43|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|T|0.40875|0.0185926580766|T|0.37511|0.1012|T|0.40788|-0.9512|SAM11_HUMAN|M|2.63|0.77240|R603S|R603S|0.28656|simple_aae|N|0.837155|0.65929|D&.&.&.&.&.|-3.31&.&.&.&.&.|9|7.5435|0.26756|0.1474:0.0:0.7184:0.1342|ENST00000455979&ENST00000342066&CCDS2.2&ENST00000341065&NM_152486.2|R462S&R603S&R603S&R510S&R603S|0.54289|0.497&0.288&0.133&0.456&0.288|||||AEFBHCI|D|0.37829|0.77508|0|0.403107|0.05239|1.000000|0.71511|0.993000|0.57359|2.102000|0.41182|1.045000|0.66922||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000420190|protein_coding|||||-/626|-/537|-/179|||COSM5053725|4625|1|cds_end_NF|SNV|HGNC|28706|||||ENSP00000411579||Q5SV95&I7FV93&A6PWC8|UPI000155D47C||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding|7/7||ENST00000455979.1:c.1388G>T|ENSP00000412228.1:p.Arg463Ser|1388/1731|1389/1626|463/541|R/S|agG/agT|COSM5053725||1|cds_start_NF|SNV|HGNC|28706|||||ENSP00000412228|||UPI000155D479||deleterious(0)|benign(0.236)|||||||||||||||||||||1|1||||||23.3|3.735147|0.50581|0.45464|0.98767157234535885|2.931379|0.146056818176487|0.47322|2.813854|0.0814994945588303|c||||5.43|3.56|0.39729|0|0.379588|0.05295|||0.999998169209764|0.74713|0|0.616487|0.41118|0|0.562822|0.20234|Sterile alpha motif domain&Sterile alpha motif/pointed domain|0.300687|0.32150|N|0.006245|T|0.40875|0.0185926580766|T|0.37511|0.1012|T|0.40788|-0.9512|SAM11_HUMAN|M|2.63|0.77240|R603S|R603S|0.28656|simple_aae|N|0.837155|0.65929|D&.&.&.&.&.|-3.31&.&.&.&.&.|9|7.5435|0.26756|0.1474:0.0:0.7184:0.1342|ENST00000455979&ENST00000342066&CCDS2.2&ENST00000341065&NM_152486.2|R462S&R603S&R603S&R510S&R603S|0.54289|0.497&0.288&0.133&0.456&0.288|||||AEFBHCI|D|0.37829|0.77508|0|0.403107|0.05239|1.000000|0.71511|0.993000|0.57359|2.102000|0.41182|1.045000|0.66922||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron|||||-/657|||||COSM5053725|1024|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron|||||-/542|||||COSM5053725|1114|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron|||||-/862|||||COSM5053725|922|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|||||-/4201|||||COSM5053725|289|-1||SNV|HGNC|24517|||||||||1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript|||||-/318|||||COSM5053725|1743|1||SNV|HGNC|28706||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron|||||-/1611|||||COSM5053725|288|-1||SNV|HGNC|24517|||||||||1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript|||||-/149|||||COSM5053725|1403|-1||SNV|HGNC|24517|||||||||1|||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000341968|promoter_flanking_region||||||||||COSM5053725||||SNV||||||||||||||||||||||||||||||||||1|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000341969|CTCF_binding_site||||||||||COSM5053725||||SNV||||||||||||||||||||||||||||||||||1|1||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:4:0,12,167 0/0:10:0,30,255 0/0:5:0,15,255 0/0:1:0,3,60 0/1:2:54,0,54 0/0:1:0,3,60 0/0:2:0,6,110 1 142961840 . C T 7.87 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=40;MQ0F=0.2;MQB=1;MQSB=0.975507;RPB=1;SGB=-0.600633;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||rs376653415||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/1:5:45,0,147 0/0:10:0,30,206 0/0:2:0,6,62 0/0:2:0,6,115 0/0:1:0,3,4 0/0:3:0,9,158 0/0:2:0,6,115 4 184366054 . G T 4.96 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T|missense_variant|MODERATE|CDKN2AIP|ENSG00000168564|Transcript|ENST00000302350|protein_coding|1/3||ENST00000302350.4:c.104G>T|ENSP00000303788.4:p.Arg35Leu|267/2646|104/381|35/126|R/L|cGc/cTc|||1||SNV|HGNC|24325|||||ENSP00000303788||Q7Z335&J3KNE1|UPI0001D3B9F8|1|deleterious(0.04)|probably_damaging(1)|Pfam_domain:PF11952&hmmpanther:PTHR16148&hmmpanther:PTHR16148:SF5|||||||||||||||||||||||||||25.7|5.263786|0.71150|0.84725|0.99757962570898917|3.276938|0.21888514118007|0.51261|2.969271|0.120829774467853|c||||5.1|4.25|0.49488|0|0.52208|0.09155|||0.999999999999999|0.74713|0|0.52208|0.09982|0|0.372554|0.05428|XRN-Two Binding Domain& XTBD|0.000000|0.62918|D|0.000006|D|0.89379|0.256732681961|T|0.60452|0.2370|T|0.62707|-0.6508|CARF_HUMAN|M|2.935|0.84897|R35L|R35L&R35L&R35L|0.81033|simple_aae&simple_aae&simple_aae|D&D&D|0.999998&1&1|0.86958|D|-3.25&-5.65&-5.65|9|15.062|0.71504|0.0:0.0:0.8568:0.1432|NM_017632.2&ENST00000504169&ENST00000302350&ENST00000510928|R35L&R35L&R35L&R35L|0.81475|0.778&0.78&0.827&0.827|||||AEFDBHCIJ|D|0.37864|0.77565|0|0.441713|0.07193|1.000000|0.71511|0.994000|0.58705|5.742000|0.68067|1.048000|0.71291||||,T|upstream_gene_variant|MODIFIER|CDKN2AIP|ENSG00000168564|Transcript|ENST00000502924|processed_transcript|||||-/347||||||1240|1||SNV|HGNC|24325|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|CDKN2AIP|ENSG00000168564|Transcript|ENST00000504169|protein_coding|1/3||ENST00000504169.1:c.104G>T|ENSP00000427108.1:p.Arg35Leu|311/2721|104/1743|35/580|R/L|cGc/cTc|||1||SNV|HGNC|24325|YES|||CCDS34110.1|ENSP00000427108|Q9NXV6|B3KTW3|UPI000004A077|1|deleterious(0)|unknown(0)|Pfam_domain:PF11952&hmmpanther:PTHR16148&hmmpanther:PTHR16148:SF5|||||||||||||||||||||||||||25.7|5.263786|0.71150|0.84725|0.99757962570898917|3.276938|0.21888514118007|0.51261|2.969271|0.120829774467853|c||||5.1|4.25|0.49488|0|0.52208|0.09155|||0.999999999999999|0.74713|0|0.52208|0.09982|0|0.372554|0.05428|XRN-Two Binding Domain& XTBD|0.000000|0.62918|D|0.000006|D|0.89379|0.256732681961|T|0.60452|0.2370|T|0.62707|-0.6508|CARF_HUMAN|M|2.935|0.84897|R35L|R35L&R35L&R35L|0.81033|simple_aae&simple_aae&simple_aae|D&D&D|0.999998&1&1|0.86958|D|-3.25&-5.65&-5.65|9|15.062|0.71504|0.0:0.0:0.8568:0.1432|NM_017632.2&ENST00000504169&ENST00000302350&ENST00000510928|R35L&R35L&R35L&R35L|0.81475|0.778&0.78&0.827&0.827|||||AEFDBHCIJ|D|0.37864|0.77565|0|0.441713|0.07193|1.000000|0.71511|0.994000|0.58705|5.742000|0.68067|1.048000|0.71291||||,T|upstream_gene_variant|MODIFIER|CDKN2AIP|ENSG00000168564|Transcript|ENST00000506835|processed_transcript|||||-/888||||||275|1||SNV|HGNC|24325|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|CDKN2AIP|ENSG00000168564|Transcript|ENST00000510928|protein_coding|1/2||ENST00000510928.1:c.104G>T|ENSP00000421308.1:p.Arg35Leu|205/860|104/408|35/135|R/L|cGc/cTc|||1||SNV|HGNC|24325|||||ENSP00000421308||D6RGD2|UPI0000E09331|1|deleterious(0.04)|probably_damaging(0.999)|hmmpanther:PTHR16148:SF5&hmmpanther:PTHR16148&Pfam_domain:PF11952|||||||||||||||||||||||||||25.7|5.263786|0.71150|0.84725|0.99757962570898917|3.276938|0.21888514118007|0.51261|2.969271|0.120829774467853|c||||5.1|4.25|0.49488|0|0.52208|0.09155|||0.999999999999999|0.74713|0|0.52208|0.09982|0|0.372554|0.05428|XRN-Two Binding Domain& XTBD|0.000000|0.62918|D|0.000006|D|0.89379|0.256732681961|T|0.60452|0.2370|T|0.62707|-0.6508|CARF_HUMAN|M|2.935|0.84897|R35L|R35L&R35L&R35L|0.81033|simple_aae&simple_aae&simple_aae|D&D&D|0.999998&1&1|0.86958|D|-3.25&-5.65&-5.65|9|15.062|0.71504|0.0:0.0:0.8568:0.1432|NM_017632.2&ENST00000504169&ENST00000302350&ENST00000510928|R35L&R35L&R35L&R35L|0.81475|0.778&0.78&0.827&0.827|||||AEFDBHCIJ|D|0.37864|0.77565|0|0.441713|0.07193|1.000000|0.71511|0.994000|0.58705|5.742000|0.68067|1.048000|0.71291||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000238686|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/1:6:42,0,220 0/0:9:0,27,255 0/0:3:0,9,168 0/0:2:0,6,120 0/0:1:0,3,60 0/0:3:0,9,151 0/0:1:0,3,49 4 190626745 . C A 4.85 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=A|downstream_gene_variant|MODIFIER|RNU1-51P|ENSG00000202215|Transcript|ENST00000365345|snRNA|||||-/176||||||3948|-1||SNV|HGNC|48393|YES|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|RP11-462G22.2|ENSG00000272566|Transcript|ENST00000608299|lincRNA|||||-/610||||||1101|-1||SNV|Clone_based_vega_gene||YES||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/1:6:42,0,197 0/0:8:0,24,254 0/0:3:0,9,170 0/0:1:0,3,60 0/0:2:0,6,120 0/0:3:0,9,169 0/0:2:0,6,120 9 131590972 . C T 10.97 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T|downstream_gene_variant|MODIFIER|CCBL1|ENSG00000171097|Transcript|ENST00000302586|protein_coding|||||-/1903|-/1269|-/422|||rs746620277|4420|-1||SNV|HGNC|1564|YES|||CCDS43884.1|ENSP00000302227|Q16773|Q9UQN7&Q9UQN6&Q5T278&Q5T276&A8K563|UPI0000073E31||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|CCBL1|ENSG00000171097|Transcript|ENST00000320665|protein_coding|||||-/1623|-/1119|-/372|||rs746620277|4426|-1||SNV|HGNC|1564||||CCDS48038.1|ENSP00000317342|Q16773|Q9UQN7&Q9UQN6|UPI0000140946||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|C9orf114|ENSG00000198917|Transcript|ENST00000361256|protein_coding||3/11|ENST00000361256.5:c.208+42G>A||-/4286|-/1131|-/376|||rs746620277||-1||SNV|HGNC|26933|YES|||CCDS6913.1|ENSP00000354812|Q5T280||UPI0000140A15||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|CCBL1|ENSG00000171097|Transcript|ENST00000436267|protein_coding|||||-/1989|-/1551|-/516|||rs746620277|4603|-1||SNV|HGNC|1564|||||ENSP00000399415||Q9UQN7&Q9UQN6&Q5T278&Q5T276&B7Z4W5&A8K563|UPI0000EE5683||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|CCBL1|ENSG00000171097|Transcript|ENST00000462722|processed_transcript|||||-/2089|||||rs746620277|4249|-1||SNV|HGNC|1564||||||||||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|C9orf114|ENSG00000198917|Transcript|ENST00000466556|retained_intron||3/5|ENST00000466556.1:n.224+42G>A||-/926|||||rs746620277||-1||SNV|HGNC|26933||||||||||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C9orf114|ENSG00000198917|Transcript|ENST00000467396|retained_intron|||||-/451|||||rs746620277|1483|-1||SNV|HGNC|26933||||||||||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C9orf114|ENSG00000198917|Transcript|ENST00000467582|protein_coding|||||-/898|-/264|-/87|||rs746620277|3871|-1|cds_start_NF|SNV|HGNC|26933|||||ENSP00000473640||R4GNG4|UPI0002B83357||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C9orf114|ENSG00000198917|Transcript|ENST00000480366|retained_intron|||||-/661|||||rs746620277|2470|-1||SNV|HGNC|26933||||||||||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|CCBL1|ENSG00000171097|Transcript|ENST00000483599|processed_transcript|||||-/2490|||||rs746620277|4430|-1||SNV|HGNC|1564||||||||||||||||||||||T:2.473e-05|T:2.485e-05|T:0|T:0|T:0|T:0|T:1.506e-05|T:0|T:0.0001214|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:7:0,21,245 0/0:5:0,15,228 0/0:4:0,12,171 0/0:1:0,3,60 0/0:1:0,3,60 0/0:3:0,9,164 0/1:4:48,0,136 15 59063889 . G T 19.94 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T|stop_gained&NMD_transcript_variant|HIGH|FAM63B|ENSG00000128923|Transcript|ENST00000316848|nonsense_mediated_decay|1/8||ENST00000316848.5:c.295G>T|ENSP00000326194.5:p.Glu99Ter|499/4866|295/1269|99/422|E/|Gag/Tag|||1||SNV|HGNC|26954|||||ENSP00000326194||J3KNL7|UPI0000374140||||hmmpanther:PTHR18063:SF8&hmmpanther:PTHR18063||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|stop_gained|HIGH|FAM63B|ENSG00000128923|Transcript|ENST00000450403|protein_coding|1/9||ENST00000450403.2:c.295G>T|ENSP00000393231.2:p.Glu99Ter|329/4820|295/1863|99/620|E/|Gag/Tag|||1||SNV|HGNC|26954||||CCDS45268.1|ENSP00000393231|Q8NBR6||UPI0000160516||||hmmpanther:PTHR18063:SF8&hmmpanther:PTHR18063|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||HC|||POSITION:0.158346752549651,T|upstream_gene_variant|MODIFIER|RP11-30K9.6|ENSG00000245975|Transcript|ENST00000500929|lincRNA|||||-/1396||||||716|-1||SNV|Clone_based_vega_gene||YES|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|stop_gained|HIGH|FAM63B|ENSG00000128923|Transcript|ENST00000559228|protein_coding|1/9||ENST00000559228.1:c.295G>T|ENSP00000452885.1:p.Glu99Ter|377/9238|295/1866|99/621|E/|Gag/Tag|||1||SNV|HGNC|26954|YES|||CCDS42046.1|ENSP00000452885|Q8NBR6||UPI0000D74C47||||hmmpanther:PTHR18063:SF8&hmmpanther:PTHR18063|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||HC|||POSITION:0.158092175777063,T|stop_gained&NMD_transcript_variant|HIGH|FAM63B|ENSG00000128923|Transcript|ENST00000560289|nonsense_mediated_decay|1/9||ENST00000560289.1:c.295G>T|ENSP00000453425.1:p.Glu99Ter|405/1859|295/1140|99/379|E/|Gag/Tag|||1||SNV|HGNC|26954|||||ENSP00000453425||H0YM15|UPI00001DFE47||||hmmpanther:PTHR18063&hmmpanther:PTHR18063:SF8||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000104485|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:4:0,12,183 0/0:7:0,21,255 0/0:2:0,6,110 0/0:2:0,6,110/1:1:60,3,0 0/0:4:0,12,220 0/0:5:0,15,255 16 68283155 . C A 17.73 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000219345|protein_coding||1/5|ENST00000219345.5:c.128-38C>A||-/2723|-/1239|-/412|||||1||SNV|HGNC|17163|YES|||CCDS10864.1|ENSP00000219345|Q8NCC3||UPI00000359EF||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000413021|protein_coding||1/4|ENST00000413021.2:c.127+3699C>A||-/1346|-/957|-/318|||||1||SNV|HGNC|17163|||||ENSP00000394197||B4DUD1|UPI00017A7E19||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000444212|protein_coding||1/1|ENST00000444212.2:c.127+3699C>A||-/943|-/639|-/212|||||1||SNV|HGNC|17163|||||ENSP00000393610||B4DPU0|UPI00017A777D||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000562966|retained_intron||1/3|ENST00000562966.1:n.175-38C>A||-/572|||||||1||SNV|HGNC|17163||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000564827|protein_coding||1/6|ENST00000564827.2:c.128-38C>A||-/781|-/727|-/242|||||1|cds_end_NF|SNV|HGNC|17163|||||ENSP00000455461||H3BPT3|UPI00024670FF||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000565744|protein_coding||1/3|ENST00000565744.1:c.128-38C>A||-/577|-/491|-/163|||||1|cds_end_NF|SNV|HGNC|17163|||||ENSP00000454227||H3BM47|UPI00024670FC||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000566188|protein_coding||1/5|ENST00000566188.1:c.128-38C>A||-/1203|-/711|-/236|||||1||SNV|HGNC|17163|||||ENSP00000457034||B4DJW4|UPI00017A70CA||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000566978|nonsense_mediated_decay||2/3|ENST00000566978.1:c.252-38C>A||-/584|-/261|-/86|||||1||SNV|HGNC|17163|||||ENSP00000457049||H3BT70|UPI00024670FD||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000568082|protein_coding||1/5|ENST00000568082.1:c.128-38C>A||-/929|-/894|-/298|||||1|cds_end_NF|SNV|HGNC|17163|||||ENSP00000454557||H3BMU8|UPI0002467100||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|PLA2G15|ENSG00000103066|Transcript|ENST00000568599|processed_transcript||1/1|ENST00000568599.1:n.407-38C>A||-/541|||||||1||SNV|HGNC|17163|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:5:0,15,255 0/0:9:0,27,255 0/0:5:0,15,208 0/0:1:0,3,60 0/0:1:0,3,600/0:2:0,6,120 0/1:2:54,0,54 17 48431266 . C A 14.18 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=A|synonymous_variant|LOW|XYLT2|ENSG00000015532|Transcript|ENST00000017003|protein_coding|2/11||ENST00000017003.2:c.411C>A|ENSP00000017003.2:p.Gly137%3D|460/3507|411/2598|137/865|G|ggC/ggA|rs544656148||1||SNV|HGNC|15517|YES|||CCDS11563.1|ENSP00000017003|Q9H1B5||UPI000013C536|1|||Lowcomplexity(Seg):seg&hmmpanther:PTHR19297&hmmpanther:PTHR19297:SF79||G:0.0002|G:0|G:0|G:0.001|G:0|G:0|||G:8.252e-05|G:9.047e-05|G:0|G:0|G:0.001218|G:0|G:0|G:0|G:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|synonymous_variant&NMD_transcript_variant|LOW|XYLT2|ENSG00000015532|Transcript|ENST00000376550|nonsense_mediated_decay|2/10||ENST00000376550.3:c.411C>A|ENSP00000365733.3:p.Gly137%3D|416/3267|411/1920|137/639|G|ggC/ggA|rs544656148||1||SNV|HGNC|15517|||||ENSP00000365733|Q9H1B5||UPI00001D68F8|1|||hmmpanther:PTHR19297&hmmpanther:PTHR19297:SF79&Lowcomplexity(Seg):seg||G:0.0002|G:0|G:0|G:0.001|G:0|G:0|||G:8.252e-05|G:9.047e-05|G:0|G:0|G:0.001218|G:0|G:0|G:0|G:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|synonymous_variant|LOW|XYLT2|ENSG00000015532|Transcript|ENST00000507602|protein_coding|2/10||ENST00000507602.1:c.411C>A|ENSP00000426501.1:p.Gly137%3D|417/2107|411/2031|137/676|G|ggC/ggA|rs544656148||1||SNV|HGNC|15517|||||ENSP00000426501||B4DT06|UPI00017A7A9F|1|||Lowcomplexity(Seg):seg&hmmpanther:PTHR19297:SF79&hmmpanther:PTHR19297||G:0.0002|G:0|G:0|G:0.001|G:0|G:0|||G:8.252e-05|G:9.047e-05|G:0|G:0|G:0.001218|G:0|G:0|G:0|G:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|XYLT2|ENSG00000015532|Transcript|ENST00000509778|protein_coding|||||-/145|-/135|-/45|||rs544656148|231|1|cds_end_NF|SNV|HGNC|15517|||||ENSP00000425511||D6RCT0|UPI0001D3B7B4|1|||||G:0.0002|G:0|G:0|G:0.001|G:0|G:0|||G:8.252e-05|G:9.047e-05|G:0|G:0|G:0.001218|G:0|G:0|G:0|G:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|XYLT2|ENSG00000015532|Transcript|ENST00000511654|nonsense_mediated_decay|||||-/587|-/354|-/117|||rs544656148|2279|1|cds_start_NF|SNV|HGNC|15517|||||ENSP00000428350||H0YB00|UPI0001E8F5AA|1|||||G:0.0002|G:0|G:0|G:0.001|G:0|G:0|||G:8.252e-05|G:9.047e-05|G:0|G:0|G:0.001218|G:0|G:0|G:0|G:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|XYLT2|ENSG00000015532|Transcript|ENST00000574840|protein_coding|||||-/901|-/141|-/46|||rs544656148|3261|1|cds_start_NF|SNV|HGNC|15517|||||ENSP00000460517||I3L3K2|UPI00025A2DC6|1|||||G:0.0002|G:0|G:0|G:0.001|G:0|G:0|||G:8.252e-05|G:9.047e-05|G:0|G:0|G:0.001218|G:0|G:0|G:0|G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:7:0,21,255 0/0:7:0,21,255 0/0:1:0,3,60 0/0:3:0,9,145 0/0:1:0,3,57 0/0:3:0,9,160 0/1:3:51,0,101 19 50215011 . G C 14.13 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=C|downstream_gene_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000295404|retained_intron|||||-/1952||||||1123|1||SNV|HGNC|18540|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000323446|protein_coding||15/18|ENST00000323446.5:c.1867-55G>C||-/2783|-/2412|-/803|||||1||SNV|HGNC|18540||||CCDS12779.1|ENSP00000319343|Q8TCG5|M0R2V3&M0R115&M0QZ13&B3KU49|UPI0000071C78|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000354199|protein_coding||16/17|ENST00000354199.5:c.1866+897G>C||-/2500|-/2145|-/714|||||1||SNV|HGNC|18540|||||ENSP00000346138|Q8TCG5|M0R2V3&M0R2H6&M0R115&M0QZ13|UPI000049E304|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000392518|protein_coding||16/19|ENST00000392518.4:c.1867-55G>C||-/2910|-/2412|-/803|||||1||SNV|HGNC|18540|YES|||CCDS12779.1|ENSP00000376303|Q8TCG5|M0R2V3&M0R115&M0QZ13&B3KU49|UPI0000071C78|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000405931|protein_coding||16/19|ENST00000405931.2:c.1834-55G>C||-/2785|-/2379|-/792|||||1||SNV|HGNC|18540||||CCDS46147.1|ENSP00000384465|Q8TCG5|M0R2V3&M0R115&M0QZ13|UPI0000072DBD|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000595031|protein_coding||6/7|ENST00000595031.1:c.732+897G>C||-/1137|-/1011|-/336|||||1|cds_start_NF|SNV|HGNC|18540|||||ENSP00000472579||M0R2H6|UPI00001410D8|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000595901|retained_intron|1/4||ENST00000595901.1:n.191G>C||191/812|||||||1||SNV|HGNC|18540|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000596701|retained_intron|9/9||ENST00000596701.1:n.2361G>C||2361/2950|||||||1||SNV|HGNC|18540|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000597099|protein_coding|||||-/310|-/246|-/81||||1239|1|cds_start_NF|SNV|HGNC|18540|||||ENSP00000471841||M0R1F9|UPI0002A4743E|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000598072|retained_intron|||||-/651||||||965|1||SNV|HGNC|18540|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000598259|nonsense_mediated_decay||17/19|ENST00000598259.1:c.*1781-55G>C||-/2679|-/207|-/68|||||1||SNV|HGNC|18540|||||ENSP00000472742||M0R0D3|UPI0000EE7A9E|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000598293|protein_coding||16/19|ENST00000598293.1:c.1867-55G>C||-/2767|-/2412|-/803|||||1||SNV|HGNC|18540||||CCDS12779.1|ENSP00000473028|Q8TCG5|M0R2V3&M0R115&M0QZ13&B3KU49|UPI0000071C78|1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000598647|retained_intron|||||-/681||||||874|1||SNV|HGNC|18540|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000599023|retained_intron|||||-/2518||||||689|1||SNV|HGNC|18540|||||||||1|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|CPT1C|ENSG00000169169|Transcript|ENST00000599937|retained_intron|||||-/700||||||801|1||SNV|HGNC|18540|||||||||1||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:6:0,18,255 0/0:5:0,15,197 0/0:1:0,3,60 0/1:3:51,0,101 0/0:1:0,3,60 0/0:5:0,15,243 0/0:4:0,12,207 19 58485425 . C A 7.47 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=A|intron_variant|MODIFIER|C19orf18|ENSG00000177025|Transcript|ENST00000314391|protein_coding||2/5|ENST00000314391.3:c.226+42G>T||-/915|-/648|-/215|||rs200465101||-1||SNV|HGNC|28642|YES|||CCDS12967.1|ENSP00000321519|Q8NEA5||UPI000006D09E||||||A:0.0002|A:0|A:0|A:0.001|A:0|A:0|||A:3.295e-05&T:8.236e-06|A:2.484e-05&T:8.28e-06|A:0&T:9.639e-05|A:8.675e-05&T:0|A:0.0001168&T:0|A:0&T:0|A:0&T:0|A:0&T:0|A:6.092e-05&T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ZNF606|ENSG00000166704|Transcript|ENST00000341164|protein_coding|||||-/4248|-/2379|-/792|||rs200465101|2996|-1||SNV|HGNC|25879|YES|||CCDS12968.1|ENSP00000343617|Q8WXB4|Q9H7U2&F8W1C8&F5H208|UPI000013C35B||||||A:0.0002|A:0|A:0|A:0.001|A:0|A:0|||A:3.295e-05&T:8.236e-06|A:2.484e-05&T:8.28e-06|A:0&T:9.639e-05|A:8.675e-05&T:0|A:0.0001168&T:0|A:0&T:0|A:0&T:0|A:0&T:0|A:6.092e-05&T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ZNF606|ENSG00000166704|Transcript|ENST00000536132|protein_coding|||||-/2417|-/2109|-/702|||rs200465101|4208|-1||SNV|HGNC|25879|||||ENSP00000445624||Q9H7U2&F5H208|UPI000206506D||||||A:0.0002|A:0|A:0|A:0.001|A:0|A:0|||A:3.295e-05&T:8.236e-06|A:2.484e-05&T:8.28e-06|A:0&T:9.639e-05|A:8.675e-05&T:0|A:0.0001168&T:0|A:0&T:0|A:0&T:0|A:0&T:0|A:6.092e-05&T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ZNF606|ENSG00000166704|Transcript|ENST00000550599|nonsense_mediated_decay|||||-/2417|-/177|-/58|||rs200465101|4208|-1||SNV|HGNC|25879|||||ENSP00000446845||F8VZG6|UPI00020CDF48||||||A:0.0002|A:0|A:0|A:0.001|A:0|A:0|||A:3.295e-05&T:8.236e-06|A:2.484e-05&T:8.28e-06|A:0&T:9.639e-05|A:8.675e-05&T:0|A:0.0001168&T:0|A:0&T:0|A:0&T:0|A:0&T:0|A:6.092e-05&T:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:6:0,18,228 0/0:3:0,9,143 0/1:5:45,0,197 0/0:3:0,9,146 0/0:1:0,3,40 0/0:4:0,12,153 0/0:3:0,9,155 20 34542161 . C A 4.93 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=A|missense_variant|MODERATE|SCAND1|ENSG00000171222|Transcript|ENST00000305978|protein_coding|2/2||ENST00000305978.2:c.46G>T|ENSP00000301995.2:p.Ala16Ser|280/902|46/540|16/179|A/S|Gcg/Tcg|||-1||SNV|HGNC|10566||||CCDS13269.1|ENSP00000301995|P57086|Q9NZG6&H0UIA5|UPI0000000C19||tolerated_low_confidence(0.09)|benign(0.283)||||||||||||||||||||||||||||10.89|1.041093|0.19381|0.34793|0.97682558830109367|0.7385781|-0.813769680502348|0.13951|0.6309112|-0.816724598787651|c|0.12588|T&.&T|2.66&.&2.66|4.83|1.56|0.22315|0|0.52208|0.09155|||0.999998482632702|0.74713|0|0.52208|0.09982|0|0.56214|0.18635||||||T|0.16687|0.00629315993648|T|0.09967|0.0234|T|0.33100|-0.9880|SCND1_HUMAN|N|0.55|0.14488|A16S|A16S&A16S|0.08979|simple_aae&simple_aae|N&N|1&1|0.14993|N&.&N|-0.46&.&-0.46|9|9.0118|0.35121|0.133:0.3212:0.5458:0.0|NM_016558.3&ENST00000305978&NM_033630.2&ENST00000373991|A16S&A16S&A79S&A16S|0.02877|0.045&0.045&0.044&0.048|||||ALL|N|0.23162|0.27820|0|0.441713|0.07193|0.000000|0.06329|0.023000|0.13823|-0.025000|0.12261|0.935000|0.48983||||,A|missense_variant|MODERATE|SCAND1|ENSG00000171222|Transcript|ENST00000373991|protein_coding|3/3||ENST00000373991.3:c.46G>T|ENSP00000363103.3:p.Ala16Ser|1117/1727|46/540|16/179|A/S|Gcg/Tcg|||-1||SNV|HGNC|10566|YES|||CCDS13269.1|ENSP00000363103|P57086|Q9NZG6&H0UIA5|UPI0000000C19||tolerated_low_confidence(0.09)|benign(0.283)||||||||||||||||||||||||||||10.89|1.041093|0.19381|0.34793|0.97682558830109367|0.7385781|-0.813769680502348|0.13951|0.6309112|-0.816724598787651|c|0.12588|T&.&T|2.66&.&2.66|4.83|1.56|0.22315|0|0.52208|0.09155|||0.999998482632702|0.74713|0|0.52208|0.09982|0|0.56214|0.18635||||||T|0.16687|0.00629315993648|T|0.09967|0.0234|T|0.33100|-0.9880|SCND1_HUMAN|N|0.55|0.14488|A16S|A16S&A16S|0.08979|simple_aae&simple_aae|N&N|1&1|0.14993|N&.&N|-0.46&.&-0.46|9|9.0118|0.35121|0.133:0.3212:0.5458:0.0|NM_016558.3&ENST00000305978&NM_033630.2&ENST00000373991|A16S&A16S&A79S&A16S|0.02877|0.045&0.045&0.044&0.048|||||ALL|N|0.23162|0.27820|0|0.441713|0.07193|0.000000|0.06329|0.023000|0.13823|-0.025000|0.12261|0.935000|0.48983||||,A|downstream_gene_variant|MODIFIER|PHF20|ENSG00000025293|Transcript|ENST00000374012|protein_coding|||||-/5922|-/3039|-/1012||||3858|1||SNV|HGNC|16098|YES|||CCDS13268.1|ENSP00000363124|Q9BVI0|Q5JXL1&Q5JWZ0&B3KUL4|UPI000006E61B||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PHF20|ENSG00000025293|Transcript|ENST00000439301|protein_coding|||||-/5824|-/819|-/272||||3873|1||SNV|HGNC|16098|||||ENSP00000410373|Q9BVI0||UPI000006FC22||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000183724|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/1:6:42,0,228 0/0:5:0,15,215 0/0:3:0,9,170 0/0:2:0,6,110 0/0:1:0,3,60 0/0:4:0,12,134 0/0:4:0,12,210 20 62076002 . C A 10.76 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000344425|protein_coding||4/7|ENST00000344425.5:c.690+10G>T||-/1423|-/1182|-/393|||rs376611221||-1||SNV|HGNC|6296||||CCDS13521.1|ENSP00000345523|O43526|Q53Y30|UPI000002A673|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000344462|protein_coding||4/15|ENST00000344462.4:c.690+10G>T||-/2750|-/2526|-/841|||rs376611221||-1||SNV|HGNC|6296||||CCDS46629.1|ENSP00000339611||Q4VXP7|UPI000002A671|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000354587|protein_coding||4/16|ENST00000354587.3:c.690+10G>T||-/3275|-/2643|-/880|||rs376611221||-1||SNV|HGNC|6296|||||ENSP00000346601||A6ND05|UPI0000D610E0|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000357249|protein_coding||4/15|ENST00000357249.2:c.690+10G>T||-/3195|-/2565|-/854|||rs376611221||-1||SNV|HGNC|6296||||CCDS13519.1|ENSP00000349789|O43526||UPI000002A66F|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000359125|protein_coding||4/16|ENST00000359125.2:c.690+10G>T||-/3249|-/2619|-/872|||rs376611221||-1||SNV|HGNC|6296|YES|||CCDS13520.1|ENSP00000352035|O43526||UPI00001279ED|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000359689|protein_coding||4/17|ENST00000359689.1:c.690+10G>T||-/3251|-/2619|-/872|||rs376611221||-1||SNV|HGNC|6296|||||ENSP00000352718||A6NM44|UPI0000456FCC|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000360480|protein_coding||4/14|ENST00000360480.3:c.690+10G>T||-/2908|-/2535|-/844|||rs376611221||-1||SNV|HGNC|6296||||CCDS13518.1|ENSP00000353668|O43526||UPI000002A670|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000370221|retained_intron||4/9|ENST00000370221.1:n.865+10G>T||-/1545|||||rs376611221||-1||SNV|HGNC|6296|||||||||1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|KCNQ2|ENSG00000075043|Transcript|ENST00000370224|protein_coding||4/15|ENST00000370224.1:c.690+10G>T||-/3015|-/2643|-/880|||rs376611221||-1||SNV|HGNC|6296|||||ENSP00000359244||Q4VXP6&Q4VXP3|UPI00004588F1|1|||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|RP11-358D14.2|ENSG00000226390|Transcript|ENST00000436263|antisense|||||-/789|||||rs376611221|3402|1||SNV|Clone_based_vega_gene||YES|||||||||||||||||||T:0.0002278|T:0|T:8.363e-06|T:0|T:0|T:0|T:0|T:0|T:0|T:0|T:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:7:0,21,255 0/0:4:0,12,182 0/0:1:0,3,60 0/1:4:48,0,152 0/0:1:0,3,60 0/0:4:0,12,161 0/0:4:0,12,201 21 37667826 . G T 10.68 . AC=1;AN=14;BQB=1;DP=50;DP4=18,6,1,0;HOB=0.0102041;ICB=0.0218487;MQ=60;MQ0F=0;MQB=1;MQSB=1;RPB=1;SGB=-0.600633;CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SRSF9P1|ENSG00000214867|Transcript|ENST00000399149|processed_pseudogene|1/1||ENST00000399149.2:n.175C>A||175/530|||||||-1||SNV|HGNC|10792|YES|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|DOPEY2|ENSG00000142197|Transcript|ENST00000399151|protein_coding|||||-/7685|-/6897|-/2298||||1254|1||SNV|HGNC|1291|YES|||CCDS13643.1|ENSP00000382104|Q9Y3R5|F8W8U9|UPI000013D876|1||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GT:DP:PL 0/0:5:0,15,212 0/0:8:0,24,255 0/0:3:0,9,169 0/0:2:0,6,120 0/0:1:0,3,60 0/1:4:48,0,158 0/0:2:0,6,110

[chapmanb]

Patrick; Thanks much, this is a big help. It looks like the interpro description from dbNSFP resulted in these blocks with spaces. I pushed a fix to the devleopment version which will skip this to avoid the problem. You can update in your current project by removing the existing VEP annotated files and re-running in place:

bcbio_nextgen.py upgrade -u development
rm -f */*-vepeffects*
bcbio_nextgen.py your_config.yaml

Hope this now works cleanly for you.

[matthdsm]

Hi,

Great this got fixed, one annotation field less, but oh well, plenty to go around!

M

[PatrickJReed]

Hi, I'm getting the same error for a different line, see below. I'm guessing its the "first 14 AA missing". This issue may effect all fields with "descriptions" ? (strings that haven't converted word separating whitespace to _), or fields that are not numeric or categorical, this one looks like MutationTaster_AAE.

[2017-02-08T02:34Z] 2017-02-08 02:34:40 ip-172-31-21-143.us-west-2.compute.internal INFO [bcbio.run.itx] - Note: -w option not given, printing list of sites... [2017-02-08T02:38Z] 2017-02-08 02:38:42 ip-172-31-21-143.us-west-2.compute.internal ERROR [bcbio.variation.recall.main] - [2017-02-08T02:38Z] htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 3298: The VCF specification does not allow for whitespace in the INFO field. Offending field value was "AC=12;AN=12;DP=96;DP4=0,0,33,15;MQ=60;MQ0F=0;MQSB=1;SGB=5.37887;VDB=0.0080319;CSQ=C|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000355826|protein_coding||2/19|ENST00000355826.5:c.282-19T>C||-/3290|-/3171|-/1056|||rs12755088||1||SNV|HGNC|30577||||CCDS53263.1|ENSP00000348081|Q96AX9|D6RFJ2&D6RE96|UPI0001C0B379|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|missense_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000357210|protein_coding|3/20||ENST00000357210.4:c.134T>C|ENSP00000349741.4:p.Met45Thr|350/3338|134/3042|45/1013|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|||||ENSP00000349741|Q96AX9|E9PD12&D6RFJ2&D6RE96|UPI00015E0B0A|1|tolerated_low_confidence(0.48)|benign(0)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||,C|missense_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000360522|protein_coding|3/19||ENST00000360522.4:c.134T>C|ENSP00000353713.4:p.Met45Thr|350/3233|134/2937|45/978|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|||||ENSP00000353713|Q96AX9|D6RFJ2&D6RE96|UPI00015E0B0B|1|tolerated_low_confidence(0.46)|benign(0.004)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||,C|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000378708|protein_coding||1/17|ENST00000378708.1:c.-22-19T>C||-/3012|-/2760|-/919|||rs12755088||1||SNV|HGNC|30577|||||ENSP00000367980||F2Z2L2&D6RFJ2&D6RE96|UPI000066D8B4|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|missense_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000378710|protein_coding|3/19||ENST00000378710.3:c.134T>C|ENSP00000367982.3:p.Met45Thr|350/3230|134/2934|45/977|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|||||ENSP00000367982|Q96AX9|F2Z2L2&D6RFJ2&D6RE96|UPI00015E0B0C|1||benign(0.004)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||,C|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000378712|protein_coding||2/17|ENST00000378712.1:c.-22-19T>C||-/2890|-/2262|-/753|||rs12755088||1||SNV|HGNC|30577||||CCDS53264.1|ENSP00000367984|Q96AX9|D6RFJ2&D6RE96|UPI00004A2928|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000464570|retained_intron|||||-/968|||||rs12755088|4110|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000467597|retained_intron|||||-/776|||||rs12755088|1332|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000473511|retained_intron|||||-/1332|||||rs12755088|4048|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000477990|retained_intron|||||-/2821|||||rs12755088|4202|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000479659|retained_intron||2/18|ENST00000479659.1:n.288-19T>C||-/4247|||||rs12755088||1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000486072|nonsense_mediated_decay|||||-/568|-/174|-/57|||rs12755088|2155|1|cds_start_NF|SNV|HGNC|30577|||||ENSP00000463504||J3QLE0|UPI000268AE05|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|start_lost&NMD_transcript_variant|HIGH|MIB2|ENSG00000197530|Transcript|ENST00000487053|nonsense_mediated_decay|3/21||ENST00000487053.1:c.2T>C|ENSP00000424615.1:p.Met1?|353/3252|2/2451|1/816|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|||||ENSP00000424615||D6RFJ2&D6RE96&D6RAZ0|UPI0001D3BC37|1|deleterious_low_confidence(0)|benign(0.042)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|missense_variant&NMD_transcript_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000489635|nonsense_mediated_decay|3/20||ENST00000489635.1:c.134T>C|ENSP00000426007.1:p.Met45Thr|269/3034|134/387|45/128|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|||||ENSP00000426007||D6RHY5|UPI0001D3BC35|1|deleterious_low_confidence(0)|benign(0.065)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||,C|intron_variant&NMD_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000502470|nonsense_mediated_decay||2/4|ENST00000502470.1:c.-22-19T>C||-/780|-/255|-/84|||rs12755088||1||SNV|HGNC|30577|||||ENSP00000423221||D6R9Q6|UPI0001D3BC38|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000503789|protein_coding||1/3|ENST00000503789.1:c.-22-19T>C||-/576|-/446|-/148|||rs12755088||1|cds_end_NF|SNV|HGNC|30577|||||ENSP00000426603||D6RFJ2|UPI0001D3BC3C|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|start_lost|HIGH|MIB2|ENSG00000197530|Transcript|ENST00000504599|protein_coding|2/19||ENST00000504599.1:c.2T>C|ENSP00000426128.1:p.Met1?|329/3311|2/2910|1/969|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|||||ENSP00000426128||E9PD12&D6RFJ2&D6RE96|UPI0001D3BC3A|1|deleterious_low_confidence(0)|benign(0)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000505370|retained_intron|||||-/809|||||rs12755088|3448|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|missense_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000505820|protein_coding|3/20||ENST00000505820.2:c.305T>C|ENSP00000426103.2:p.Met102Thr|322/3305|305/3213|102/1070|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577|YES|||CCDS41224.2|ENSP00000426103|Q96AX9|E9PD12&D6RFJ2&D6RE96|UPI0001C0B37A|1|tolerated_low_confidence(0.23)|benign(0.007)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||,C|intron_variant&NMD_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000506488|nonsense_mediated_decay||1/16|ENST00000506488.1:c.-22-19T>C||-/2997|-/1188|-/395|||rs12755088||1||SNV|HGNC|30577|||||ENSP00000425032||D6RFJ2&D6RED3&D6RE96|UPI0001D3BC3D|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000507229|retained_intron|2/14||ENST00000507229.1:n.328T>C||328/2582|||||rs12755088||1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000508148|retained_intron|||||-/577|||||rs12755088|1675|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000508455|retained_intron|||||-/555|||||rs12755088|169|1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000510793|protein_coding||1/3|ENST00000510793.1:c.-22-19T>C||-/889|-/526|-/175|||rs12755088||1|cds_end_NF|SNV|HGNC|30577|||||ENSP00000426865||D6RFJ2&D6RE96|UPI0001D3BC39|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000511502|retained_intron|3/19||ENST00000511502.1:n.251T>C||251/3326|||||rs12755088||1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000512004|processed_transcript|1/3||ENST00000512004.1:n.291T>C||291/598|||||rs12755088||1||SNV|HGNC|30577|||||||||1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000514234|protein_coding|||||-/2562|-/2490|-/829|||rs12755088|390|1|cds_start_NF|SNV|HGNC|30577|||||ENSP00000427680|||UPI0001D3BC3F|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000514363|nonsense_mediated_decay||2/5|ENST00000514363.1:c.111-19T>C||-/592|-/345|-/114|||rs12755088||1||SNV|HGNC|30577|||||ENSP00000420935||D6RDI1|UPI0001D3BC36|1|||||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||,C|missense_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000518681|protein_coding|3/19||ENST00000518681.1:c.305T>C|ENSP00000428264.1:p.Met102Thr|328/3116|305/3018|102/1005|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577||||CCDS53262.1|ENSP00000428264|Q96AX9|D6RFJ2&D6RE96|UPI0001C0B37B|1|tolerated_low_confidence(0.8)|benign(0.001)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||,C|missense_variant|MODERATE|MIB2|ENSG00000197530|Transcript|ENST00000520777|protein_coding|3/20||ENST00000520777.1:c.305T>C|ENSP00000428660.1:p.Met102Thr|350/3321|305/3201|102/1066|M/T|aTg/aCg|rs12755088||1||SNV|HGNC|30577||||CCDS53261.1|ENSP00000428660|Q96AX9|D6RFJ2&D6RE96|UPI0001C0B378|1|tolerated_low_confidence(0.24)|benign(0.001)|||T:0.2264|C:0.7057|C:0.8674|C:0.5516|C:0.9364|C:0.8599|C:0.7668|C:0.9401|C:0.862&G:3.715e-04|C:0.8797&G:0.0004216|C:0.7673&G:0|C:0.8125&G:0|C:0.6241&G:0.006096|C:0.9004&G:0|C:0.9411&G:0|C:0.9115&G:0|C:0.8605&G:0|||||||||0.012|-1.067061|0.02948|0.09656|0.72446153597339691|0.1439896|-1.41507211592796|0.03047|0.1422915|-1.34334199252917|c|0.34443|T&T&T&T|1.36&1.42&1.36&1.44|1.5|-2.47|0.06037|0|0.709663|0.81062|ENSG00000269227.1|Thyroid|0.00575142636992884|0.11063|0|0.645312|0.48411|0|0.655142|0.61628|3.416180|0.02838|U|0.135053||||T|0.00011|0.0000|T|0.30025|-0.9996|MIB2_HUMAN|N|0|0.06535|M45T|first 14 AA missing&M45T&M45T&M102T&M102T&M102T&M45T&.&.&.|0.08979|complex_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&simple_aae&without_aae&without_aae&without_aae|P&P&P&P&P&P&P&P&P&P|1&1&1&1&1&1&1&1&1&1|0.09314|N|0.21&0.11&0.21&-0.15|9|4.7295|0.12251|0.609:0.0:0.0:0.391|ENST00000357210&ENST00000360522&ENST00000487053&ENST00000505820&ENST00000489635&NM_001170686.1&NM_080875.2&ENST00000518681&ENST00000504599&NM_001170688.1&ENST00000378710&ENST00000520777|M45T&M45T&M1T&M102T&M45T&M102T&M102T&M102T&M1T&M102T&M45T&M102T|0.14854|0.062&0.071&0.091&0.055&0.13&0.037&0.037&0.089&0.087&0.037&0.062&0.089|||||AEFBI|N|0.01140|0.00195|0|0.706298|0.60946|0.000000|0.06329|0.002000|0.06231|-0.194000|0.09480|-1.025000|0.02104||||", for input source: /efs/Kindred87/work/bcbiotx/tmpjltl0j/Kindred_87-ensemble-work/Kindred_87-samtools-nofilter.vcf.gz

[chapmanb]

Patrick; Thanks for the heads up on the issue. I removed this problem field as well and hopefully that'll do it. If we keep running into a lot of edge cases with these we might need to look at going back to the previous restricted set and only adding new values if we're sure they avoid this. Thanks again.

[matthdsm]

Hi Brad, Patrick,

Still thinks it's weird we're getting these issues now. I've been pondering an alternate approach for dbNSFP, using vcfanno. This has worked well in my tests, en quite fast too I might add. But then again, dbNSFP didn't give me any issues with VEP too, although it has proven to be very unreliable in the past..

M

[PatrickJReed]

I ran into another field with whitespace in it so i've rolled back to the stable version for the time being.

[chapmanb]

Patrick -- sorry about the continued problems. Matthias, at this point we probably need to roll back the dbNSFP fields supplied to VEP so we're including a smaller subset that we can validate don't have whitespace in them. If we revert to the previous list of dbNSFP fields would this work for you? Are there any of the additional ones you need for your analyses?

[matthdsm]

Hi Brad, I'd really like to keep the list as expansive as possible, since our clinicians like to have a lot of options. That being said, I completely understand if you'd like to revert to the a list of which you know it works. I'll leave this choice u to you.

On a related note, how would you feel about moving the dbNSFP annotation from VEP to vcfanno? I've found vcfanno to be much more speedy and way more reliable when it comes to dbNSFP. This way, people who prefer to use SnpEff could also benefit from dbNSFP annotations. I have a vcfanno config ready for dbNSFP/dbscSNV if you'd like to have it.

Cheers, M

[chapmanb]

Patrick and Mathias; Thanks again for the feedback, I've rolled this back to the previous annotations that we've tested as working. Matthias, if you want to include additional fields that clinicians find useful then we can definitely do this and test as they go.

Having dbNSFP annotations in a vcfanno/gemini approach would be great to have. I'd be happy to figure out how to include that in the current pipeline and we can discuss more in #1573

[pfpjs]

Hi all,

I just hit this bug during the creation of the GEMINI db of 6 WES trios (using the old approach, not vcf2db). On a side note, this was the first time dbNSFP annotations worked, so I was feeling hopeful.

Since dbNSFP is heavily processed during download (at least for hg19/GRCh37), would it be feasible to s/ /_/ during this processing step?

[chapmanb]

Paulo; I just reverted this to the old set of annotations so if you update to latest-devel, remove the old VEP files and re-run:

bcbio_nextgen.py upgrade -u development
rm -f */*-vepeffects*

It should hopefully work now. Sorry about the issues and hope this fixes it.