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Variant Discovery in High-Throughput Sequencing Data

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The provided reference alleles do not appear to represent the same position, CTA* vs. CTT*

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14 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi Oliver Ruebenacker,

    This error message is indicating that there is something wrong with your data. At the location mentioned in the error message, there is a reference mismatch issue. It looks related to a previous bug fix we put out in VariantRecalibrator to supply the location when this error comes up. https://gatk.broadinstitute.org/hc/en-us/community/posts/360074618292-New-version-of-GATK-leads-to-VariantRecalibrator-error-

    Is there something with these two samples that could have led to this reference mismatch problem?

    Best,

    Genevieve

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    Oliver Ruebenacker

    Hello,

    I used GATK Best Practices workflows from beginning to end, including using the reference data that were provided with these workflows. If the references are inconsistent, how can this be caused by my sequencing data? Thanks!

    Best, Oliver

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  • Avatar
    Oliver Ruebenacker

    Hello,

    For 2-1-Processing-For-Variant-Discovery-B37, the input "hg38" for ref_name looks suspicious. Is it incorrect and is the correct value "b37"?

    Could this be the cause for the error?

    Thanks!

    Best, Oliver

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  • Avatar
    Genevieve Brandt (she/her)

    Yes, there might be an issue with how you are running the featured workspace. I'm looking into this further and will let you know when I have an update.

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  • Avatar
    Oliver Ruebenacker

    Thanks, looking forward!

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  • Avatar
    Samantha (she/her)

    Hi Oliver Ruebenacker,

    Are you running the workflow on Terra? If so, can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Toggle the "Share with support" button to "Yes"
    2. Click Save

    Please provide us with a link to your workspace. We’ll be happy to take a closer look as soon as we can!

    Best,

    Samantha

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  • Avatar
    Oliver Ruebenacker

    Hello,

    The workspace is here: https://app.terra.bio/#workspaces/amp-dcc-rfp15/Pollak_Nephrotic_Syndrome_Portal

    The submission with the error is here: https://app.terra.bio/#workspaces/amp-dcc-rfp15/Pollak_Nephrotic_Syndrome_Portal/job_history/be0a714d-c873-4fc9-b20c-32c3cce1f5b0

    And the workspace is shared with support now.

    Thanks for looking into this!

    Best, Oliver

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  • Avatar
    Oliver Ruebenacker

    Hello,

    I was wondering if there is any update on this? Thanks!

    Best, Oliver

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  • Avatar
    Samantha (she/her)

    Hi Oliver,

    Sorry for the delayed response. It does seem like there is an error in the Featured Workspace where the ref_name input for the 2-1-Processing-For-Variant-Discovery-B37 workflow is incorrectly set to "hg38." The inputs.json in Github for this workflow does indeed set ref_name to "b37": https://github.com/gatk-workflows/gatk4-data-processing/blob/2.1.0/processing-for-variant-discovery-gatk4.b37.wgs.inputs.json.

    I'll make this update in the workspace and test it out, but in the meantime, you can update the input in your workspace and try re-running the pipeline.

    Best,

    Samantha

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    Oliver Ruebenacker

    Hello,

    I reran it with "b37", but I'm still getting this error. Any ideas? Thanks!

    2022/05/07 20:07:54 Starting container setup.
    2022/05/07 20:07:56 Done container setup.
    2022/05/07 20:07:58 Starting localization.
    2022/05/07 20:08:08 Localization script execution started...
    2022/05/07 20:08:08 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz
    2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
    2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx
    2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf
    2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi
    2022/05/07 20:08:11 Localizing input gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi -> /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi
    Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz...
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    Operation completed over 1 objects/1.4 GiB.                                      
    / [1 files][  1.4 GiB/  1.4 GiB]   64.6 MiB/s                                   
    Copying gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx...
    / [1 files][  1.4 GiB/  1.4 GiB]   64.5 MiB/s                                   
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    Copying gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf...
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    Copying gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi...
    / [3 files][  1.5 GiB/  1.5 GiB]   43.2 MiB/s                                   
    / [4 files][  1.5 GiB/  1.5 GiB]   41.2 MiB/s                                   
    ==> NOTE: You are performing a sequence of gsutil operations that may
    run significantly faster if you instead use gsutil -m cp ... Please
    see the -m section under "gsutil help options" for further information
    about when gsutil -m can be advantageous.
    
    Copying gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi...
    / [4 files][  1.5 GiB/  1.5 GiB]   41.0 MiB/s                                   
    / [5 files][  1.5 GiB/  1.5 GiB]   38.2 MiB/s                                   
    2022/05/07 20:08:38 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz.tbi
    2022/05/07 20:08:39 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -> /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz
    Copying gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz...
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    Operation completed over 1 objects/258.6 MiB.                                    
    \ [1 files][258.6 MiB/258.6 MiB]                                                
    2022/05/07 20:08:45 Localizing input gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/script -> /cromwell_root/script
    2022/05/07 20:08:47 Localization script execution complete.
    2022/05/07 20:08:51 Done localization.
    2022/05/07 20:08:52 Running user action: docker run -v /mnt/local-disk:/cromwell_root -v /mnt/d-c74a541aa27f13cfe59c2f998a664729:/mnt/d9e025138b28caa42dd4006fc3636661:ro --entrypoint=/bin/bash broadinstitute/gatk@sha256:5c8ad33becf8541ede410de4c99b861ae13bbb0a2dfa7501dcd758be8fc3f36d /cromwell_root/script
    Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.df55fe54
    20:08:56.917 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
    20:08:57.090 INFO  VariantRecalibrator - ------------------------------------------------------------
    20:08:57.091 INFO  VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.4.0
    20:08:57.091 INFO  VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
    20:08:57.091 INFO  VariantRecalibrator - Executing as root@d31f73fa6011 on Linux v5.10.107+ amd64
    20:08:57.091 INFO  VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
    20:08:57.092 INFO  VariantRecalibrator - Start Date/Time: May 7, 2022 8:08:56 PM GMT
    20:08:57.092 INFO  VariantRecalibrator - ------------------------------------------------------------
    20:08:57.092 INFO  VariantRecalibrator - ------------------------------------------------------------
    20:08:57.093 INFO  VariantRecalibrator - HTSJDK Version: 2.24.1
    20:08:57.093 INFO  VariantRecalibrator - Picard Version: 2.25.4
    20:08:57.093 INFO  VariantRecalibrator - Built for Spark Version: 2.4.5
    20:08:57.094 INFO  VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
    20:08:57.094 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
    20:08:57.094 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
    20:08:57.094 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
    20:08:57.094 INFO  VariantRecalibrator - Deflater: IntelDeflater
    20:08:57.094 INFO  VariantRecalibrator - Inflater: IntelInflater
    20:08:57.095 INFO  VariantRecalibrator - GCS max retries/reopens: 20
    20:08:57.095 INFO  VariantRecalibrator - Requester pays: disabled
    20:08:57.095 INFO  VariantRecalibrator - Initializing engine
    20:08:57.419 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf
    20:08:57.481 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz
    20:08:57.552 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
    20:08:57.684 INFO  FeatureManager - Using codec VCFCodec to read file file:///cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz
    20:08:57.896 INFO  VariantRecalibrator - Done initializing engine
    20:08:57.900 INFO  TrainingSet - Found mills track: 	Known = false 	Training = true 	Truth = true 	Prior = Q12.0
    20:08:57.900 INFO  TrainingSet - Found axiomPoly track: 	Known = false 	Training = true 	Truth = false 	Prior = Q10.0
    20:08:57.900 INFO  TrainingSet - Found dbsnp track: 	Known = true 	Training = false 	Truth = false 	Prior = Q2.0
    20:08:57.914 WARN  GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
    20:08:57.934 INFO  ProgressMeter - Starting traversal
    20:08:57.934 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
    20:08:59.193 INFO  VariantRecalibrator - Shutting down engine
    [May 7, 2022 8:08:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.04 minutes.
    Runtime.totalMemory()=24696061952
    org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at 1:3418656 [VC /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz @ 1:3418656 Q49.04 of type=SNP alleles=[C*, T] attr={AC=2, AF=0.020, AN=100, AS_BaseQRankSum=., AS_FS=0.000, AS_InbreedingCoeff=0.3892, AS_MQ=60.00, AS_MQRankSum=., AS_QD=28.53, AS_ReadPosRankSum=., AS_SOR=0.693, DP=137, ExcessHet=0.0000, FS=0.000, InbreedingCoeff=0.3892, MLEAC=5, MLEAF=0.050, MQ=60.00, QD=35.48, SOR=1.609} GT=[] filters=
    	at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)
    	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
    	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    	at java.util.Iterator.forEachRemaining(Iterator.java:116)
    	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
    	at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
    	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
    	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
    	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    	at org.broadinstitute.hellbender.Main.main(Main.java:289)
    Caused by: java.lang.IllegalStateException: Reference allele mismatch at position 1:3418653 : 
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:427)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.parseTrainingSets(VariantDataManager.java:399)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:615)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:578)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:543)
    	at java.util.ArrayList.forEach(ArrayList.java:1257)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:543)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:522)
    	at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139)
    	... 20 more
    Caused by: java.lang.IllegalStateException: The provided reference alleles do not appear to represent the same position, CCG* vs. CGC*
    	at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.determineReferenceAllele(GATKVariantContextUtils.java:237)
    	at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.isAlleleInList(GATKVariantContextUtils.java:166)
    	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.doAllelesMatch(VariantDataManager.java:425)
    	... 28 more
    Using GATK jar /gatk/gatk-package-4.2.4.0-local.jar
    Running:
        java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms24g -jar /gatk/gatk-package-4.2.4.0-local.jar VariantRecalibrator -V /cromwell_root/fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-SitesOnlyGatherVcf/neph.sites_only.vcf.gz -O neph.indels.recal --tranches-file neph.indels.tranches --trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 97.0 -tranche 96.0 -tranche 95.0 -tranche 94.0 -tranche 93.5 -tranche 93.0 -tranche 92.0 -tranche 91.0 -tranche 90.0 -an FS -an ReadPosRankSum -an MQRankSum -an QD -an SOR -an DP --use-allele-specific-annotations -mode INDEL --max-gaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12 /cromwell_root/gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf -resource:axiomPoly,known=false,training=true,truth=false,prior=10 /cromwell_root/gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz -resource:dbsnp,known=true,training=false,truth=false,prior=2 /cromwell_root/gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz
    2022/05/07 20:09:03 Starting delocalization.
    2022/05/07 20:09:04 Delocalization script execution started...
    2022/05/07 20:09:04 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/memory_retry_rc
    2022/05/07 20:09:06 Delocalizing output /cromwell_root/rc -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/rc
    2022/05/07 20:09:08 Delocalizing output /cromwell_root/stdout -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/stdout
    2022/05/07 20:09:10 Delocalizing output /cromwell_root/stderr -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/stderr
    2022/05/07 20:09:11 Delocalizing output /cromwell_root/neph.indels.recal -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/neph.indels.recal
    2022/05/07 20:09:13 Delocalizing output /cromwell_root/neph.indels.recal.idx -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/neph.indels.recal.idx
    2022/05/07 20:09:14 Delocalizing output /cromwell_root/neph.indels.tranches -> gs://fc-016ff50b-080a-4838-95cd-801061ce2464/12d05288-28c3-41b1-99fb-28b7055a979f/JointGenotyping/1f1915e4-767c-49ec-98e1-67bc2f8e6797/call-IndelsVariantRecalibrator/neph.indels.tranches
    2022/05/07 20:09:16 Delocalization script execution complete.
    2022/05/07 20:09:17 Done delocalization.
    

    Best, Oliver

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    Genevieve Brandt (she/her)

    Hi Oliver Ruebenacker, thanks for the update. We're doing some testing to determine if this issue is coming from the featured workspace or your input data.

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    Oliver Ruebenacker

    Hello Genevieve,

    Thanks for the update and I'm looking forward to the results of the test!

    We've also looked deeper into the issue, and we noticed that while the variant called by GATK looked like this:

    1       3418653 .       CCG     C       77.64   PASS    AC=1;AF=0.010;AN=100;AS_BaseQRankSum=-0.500;AS_FS=0.000;AS_InbreedingCoeff=0.3458;AS_MQ=60.00;AS_MQRankSum=1.200;AS_QD=13.00;AS_ReadPosRankSum=-0.900;AS_SOR=0.693;BaseQRankSum=-4.310e-01;DP=171;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.3458;MLEAC=5;MLEAF=0.050;MQ=54.09;MQRankSum=1.28;QD=12.94;ReadPosRankSum=-8.420e-01;SOR=0.693

    The file dbsnp_138.b37.vcf.gz provided as reference by Terra and included as input to the failing task looks like this:

    1       3418653 rs369335009     CGC     C,CG    .       .       NOC;OTHERKG;RS=369335009;RSPOS=3418654;SAO=0;SSR=0;VC=DIV;VP=0x050000000001000002000210;WGT=1;dbSNPBuildID=138

    So indeed there is a conflict. One solution might be to upgrade to a later dbsnp file.

    Thanks!

    Best, Oliver

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    Samantha (she/her)

    Hi Oliver Ruebenacker,

    Sorry for the delay. We are still looking into this and will let you know once we have an update.

    Best,

    Samantha

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    Samantha (she/her)

    Hi Oliver Ruebenacker,

    I've confirmed with the pipeline authors that the dbsnp file is indeed incorrect. I'll work on getting this updated in the featured workspace. Thank you for pointing this out!

    Best,

    Samantha

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