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Reading Vcf Files from Strelka

LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie, Cancer Tools Developer
edited August 2013 in Ask the GATK team

Strelka produces vcf files that GATK has issues with. The files pass vcftools validation, which according to the docs is the official validation, they do not pass ValidateVariants. VariantEval can't read them either. I'm unsure where the bug lives.

vcf file looks like this:

##fileformat=VCFv4.1
##fileDate=20130801
##source=strelka
##source_version=2.0.8
##startTime=Thu Aug  1 15:23:54 2013
##reference=file:///xchip/cga_home/louisb/reference/human_g1k_v37_decoy.fasta
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##content=strelka somatic indel calls
##germlineIndelTheta=0.0001
##priorSomaticIndelRate=1e-06
##INFO=<ID=QSI,Number=1,Type=Integer,Description="Quality score for any somatic variant, ie. for the ALT haplotype to be present at a significantly different frequency in the tumor and normal">
##INFO=<ID=TQSI,Number=1,Type=Integer,Description="Data tier used to compute QSI">
##INFO=<ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
##INFO=<ID=QSI_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
##INFO=<ID=TQSI_NT,Number=1,Type=Integer,Description="Data tier used to compute QSI_NT">
##INFO=<ID=SGT,Number=1,Type=String,Description="Most likely somatic genotype excluding normal noise states">
##INFO=<ID=RU,Number=1,Type=String,Description="Smallest repeating sequence unit in inserted or deleted sequence">
##INFO=<ID=RC,Number=1,Type=Integer,Description="Number of times RU repeats in the reference allele">
##INFO=<ID=IC,Number=1,Type=Integer,Description="Number of times RU repeats in the indel allele">
##INFO=<ID=IHP,Number=1,Type=Integer,Description="Largest reference interupted homopolymer length intersecting with the indel">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
##INFO=<ID=OVERLAP,Number=0,Type=Flag,Description="Somatic indel possibly overlaps a second indel.">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth for tier1">
##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2">
##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
##FILTER=<ID=Repeat,Description="Sequence repeat of more than 8x in the reference sequence">
##FILTER=<ID=iHpol,Description="Indel overlaps an interupted homopolymer longer than 14x in the reference sequence">
##FILTER=<ID=BCNoise,Description="Average fraction of filtered basecalls within 50 bases of the indel exceeds 0.3">
##FILTER=<ID=QSI_ref,Description="Normal sample is not homozygous ref or sindel Q-score < 30, ie calls with NT!=ref or QSI_NT < 30">
##cmdline=/xchip/cga_home/louisb/Strelka/strelka_workflow_1.0.7/libexec/consolidateResults.pl --config=/xchip/cga/benchmark/testing/full-run/somatic-benchmark/spiked/Strelka_NDEFGHI_T12345678_0.8/config/run.config.ini
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR
1   797126  .   GTAAT   G   .   PASS    IC=1;IHP=2;NT=ref;QSI=56;QSI_NT=56;RC=2;RU=TAAT;SGT=ref-        >het;SOMATIC;TQSI=1;TQSI_NT=1   DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50   47:47:48,49:0,0:3,3:48.72:0.00:0.00 62:62:36,39:17,19:9,9:42.49:0.21:0.00``

The output I get from ValidateVariants is

java -jar ~/Workspace/gatk-protected/dist/GenomeAnalysisTK.jar -T ValidateVariants --variant strelka1.vcf -R ~/cga_home/reference/human_g1k_v37_decoy.fasta
    INFO  17:19:45,289 HelpFormatter - --------------------------------------------------------------------------------
    INFO  17:19:45,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/22 11:08:15
    INFO  17:19:45,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  17:19:45,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  17:19:45,295 HelpFormatter - Program Args: -T ValidateVariants --variant strelka1.vcf -R /Users/louisb/cga_home/reference/human_g1k_v37_decoy.fasta
    INFO  17:19:45,295 HelpFormatter - Date/Time: 2013/08/28 17:19:45
    INFO  17:19:45,295 HelpFormatter - --------------------------------------------------------------------------------
    INFO  17:19:45,295 HelpFormatter - --------------------------------------------------------------------------------
    INFO  17:19:45,300 ArgumentTypeDescriptor - Dynamically determined type of strelka1.vcf to be VCF
    INFO  17:19:45,412 GenomeAnalysisEngine - Strictness is SILENT
    INFO  17:19:45,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO  17:19:45,533 RMDTrackBuilder - Loading Tribble index from disk for file strelka1.vcf
    INFO  17:19:45,615 GenomeAnalysisEngine - Preparing for traversal
    INFO  17:19:45,627 GenomeAnalysisEngine - Done preparing for traversal
    INFO  17:19:45,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO  17:19:45,627 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
    INFO  17:19:46,216 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 2.7-1-g42d771f):
    ##### ERROR
    ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
    ##### ERROR The error message below tells you what is the problem.
    ##### ERROR
    ##### ERROR If the problem is an invalid argument, please check the online documentation guide
    ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ##### ERROR
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ##### ERROR
    ##### ERROR MESSAGE: File /Users/louisb/Workspace/strelkaVcfDebug/strelka1.vcf fails strict validation: one or more of the ALT allele(s) for the record at position 1:797126 are not observed at all in the sample genotypes
    ##### ERROR ------------------------------------------------------------------------------------------

output from VariantEval is:

java -jar ~/Workspace/gatk-protected/dist/GenomeAnalysisTK.jar -T VariantEval --eval strelka1.vcf -R ~/cga_home/reference/human_g1k_v37_decoy.fasta
INFO  17:15:44,333 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:15:44,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-1-g42d771f, Compiled 2013/08/22 11:08:15
INFO  17:15:44,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  17:15:44,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  17:15:44,339 HelpFormatter - Program Args: -T VariantEval --eval strelka1.vcf -R /Users/louisb/cga_home/reference/human_g1k_v37_decoy.fasta
INFO  17:15:44,339 HelpFormatter - Date/Time: 2013/08/28 17:15:44
INFO  17:15:44,339 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:15:44,339 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:15:44,349 ArgumentTypeDescriptor - Dynamically determined type of strelka1.vcf to be VCF
INFO  17:15:44,476 GenomeAnalysisEngine - Strictness is SILENT
INFO  17:15:44,603 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  17:15:44,623 RMDTrackBuilder - Loading Tribble index from disk for file strelka1.vcf
INFO  17:15:44,710 GenomeAnalysisEngine - Preparing for traversal
INFO  17:15:44,722 GenomeAnalysisEngine - Done preparing for traversal
INFO  17:15:44,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  17:15:44,723 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
INFO  17:15:44,831 VariantEval - Creating 3 combinatorial stratification states
INFO  17:15:45,382 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: BUG: Unexpected genotype type: [NORMAL NA DP 47 {DP2=47, DP50=48.72, FDP50=0.00, SUBDP50=0.00, TAR=48,49, TIR=0,0, TOR=3,3}]
    at org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.CountVariants.update1(CountVariants.java:201)
    at org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext.apply(EvaluationContext.java:88)
    at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.map(VariantEval.java:455)
    at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.map(VariantEval.java:124)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.7-1-g42d771f):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: BUG: Unexpected genotype type: [NORMAL NA DP 47 {DP2=47, DP50=48.72, FDP50=0.00, SUBDP50=0.00, TAR=48,49, TIR=0,0, TOR=3,3}]
##### ERROR ------------------------------------------------------------------------------------------
Post edited by LouisB on

Best Answer

Answers

  • LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie, Cancer Tools Developer

    Is there an easy way to coerce Strelka output into a format that VariantEval wouldn't mind? It doesn't seem like I actually need to know the genotyping information if I just want to count indel lengths and concordance between call sets?

  • ebanksebanks Posts: 679GATK Developer mod

    If the VCF is valid then the GATK should be able to read it. Can you please post the error message here?

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie, Cancer Tools Developer

    I posted it in my first post, is it not visible?

    java -jar ../gatk-protected/dist/GenomeAnalysisTK.jar -T VariantEval -R ~/cga_home/reference/human_g1k_v37_decoy.fasta --eval strelka1.vcf
    INFO  10:41:22,868 HelpFormatter - --------------------------------------------------------------------------------
    INFO  10:41:22,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/29 10:02:59
    INFO  10:41:22,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO  10:41:22,870 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO  10:41:22,874 HelpFormatter - Program Args: -T VariantEval -R /Users/louisb/cga_home/reference/human_g1k_v37_decoy.fasta --eval strelka1.vcf
    INFO  10:41:22,875 HelpFormatter - Date/Time: 2013/08/29 10:41:22
    INFO  10:41:22,875 HelpFormatter - --------------------------------------------------------------------------------
    INFO  10:41:22,875 HelpFormatter - --------------------------------------------------------------------------------
    INFO  10:41:22,887 ArgumentTypeDescriptor - Dynamically determined type of strelka1.vcf to be VCF
    INFO  10:41:22,996 GenomeAnalysisEngine - Strictness is SILENT
    INFO  10:41:23,167 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO  10:41:23,187 RMDTrackBuilder - Loading Tribble index from disk for file strelka1.vcf
    INFO  10:41:23,266 GenomeAnalysisEngine - Preparing for traversal
    INFO  10:41:23,278 GenomeAnalysisEngine - Done preparing for traversal
    INFO  10:41:23,278 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO  10:41:23,278 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
    INFO  10:41:23,334 VariantEval - Creating 3 combinatorial stratification states
    INFO  10:41:24,307 GATKRunReport - Uploaded run statistics report to AWS S3
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: BUG: Unexpected genotype type: [NORMAL NA DP 47 {DP2=47, DP50=48.72, FDP50=0.00, SUBDP50=0.00, TAR=48,49, TIR=0,0, TOR=3,3}]
        at org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.CountVariants.update1(CountVariants.java:201)
        at org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext.apply(EvaluationContext.java:88)
        at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.map(VariantEval.java:455)
        at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.map(VariantEval.java:124)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
        at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.7-2-g6bda569):
    ##### ERROR
    ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ##### ERROR Visit our website and forum for extensive documentation and answers to
    ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ##### ERROR
    ##### ERROR MESSAGE: BUG: Unexpected genotype type: [NORMAL NA DP 47 {DP2=47, DP50=48.72, FDP50=0.00, SUBDP50=0.00, TAR=48,49, TIR=0,0, TOR=3,3}]
    ##### ERROR ------------------------------------------------------------------------------------------
    
  • LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie, Cancer Tools Developer

    Ok, Kurt was right about this. It does run fine if you leave out CountVariants, which was looking for genotype information and then failing. I should have looked into the stack trace before posting.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,073Administrator, GATK Developer admin

    Hey @LouisB, could you send us a file snippet so we can reproduce the issue locally? The user error from strict validation is technically correct, but VariantEval should give a better error.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,073Administrator, GATK Developer admin

    Or you could go ahead and send us a patch that fixes the problem... very cool, thanks!

    Geraldine Van der Auwera, PhD

  • LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie, Cancer Tools Developer

    @Geraldine_VdAuwera Are the 3 code blocks in my first post not visible to anyone? I posted the vcf, and the output from the VariantEval and the validator, but it seems like no one can see them. They show up for me. Also, the forum bars you from uploading vcf files. (I'm sure you can rename them as .txt, but that's kind of confusing for viewers.)

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,073Administrator, GATK Developer admin

    Hi @LouisB,

    Your code blocks are visible, yes. I can't speak for the others, but some who jumped in mid-thread might not have read everything and missed it. For my part, I originally asked for the vcf files as a separate upload because copying text straight from the forum messes up the formatting, which is a waste of time to fix.

    Yeah, the forum is picky about file types for security reasons (and size is also constrained). Typically we ask that people upload their test files to our FTP server; in your case I thought you might just send me a link to a file on /humgen. Ultimately we want to set up a better solution than the FTP because it's pretty clunky...

    Geraldine Van der Auwera, PhD

  • LouisBLouisB Broad InstitutePosts: 25Member, Third-party Developer, GSA Collaborator, Broadie, Cancer Tools Developer

    @Geraldine_VdAuwera Thanks, I wasn't thinking about the formatting issues. I'll post links to files in the future.

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