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CalculateGenotypePosteriors (hg19) error

sbourgeoissbourgeois London, UKMember
edited July 2017 in Ask the GATK team

Hi,

I converted 1000G_phase3_v4_20130502.sites.vcf to hg19 using Picard 2.10.0 with the following command:

java -Xincgc -Xmx5G -jar /data/home/hhx037/picard-tools/picard.jar LiftoverVcf \
   I=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/b37/1000G_phase3_v4_20130502.sites.vcf \
   O=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.sites.vcf \
   CHAIN=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/liftover/b37tohg19.chain \
   REJECT=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.liftover_rejected.vcf \
   R=/data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta

and when running CalculateGenotypePosteriors I get the following error:

OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
OpenJDK 64-Bit Server VM warning: If the number of processors is expected to increase from one, then you should configure the number of parallel GC threads appropriately using -XX:ParallelGCThreads=N
INFO 13:02:12,260 HelpFormatter - ----------------------------------------------------------------------------------
INFO 13:02:12,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 13:02:12,267 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 13:02:12,267 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 13:02:12,267 HelpFormatter - [Sat Jul 08 13:02:12 BST 2017] Executing on Linux 3.10.0-514.16.1.el7.x86_64 amd64
INFO 13:02:12,267 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_131-b12
INFO 13:02:12,270 HelpFormatter - Program Args: -T CalculateGenotypePosteriors -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -V /data/WHRI-Panos-Scratch/hhx037/piperi/filtered/piperi_snps_indels.vcf --supporting /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.sites.vcf -ped /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped -o ./refined/piperi_snps_indels.postCGP.vcf
INFO 13:02:12,274 HelpFormatter - Executing as hhx037@nxv27 on Linux 3.10.0-514.16.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b12.
INFO 13:02:12,275 HelpFormatter - Date/Time: 2017/07/08 13:02:12
INFO 13:02:12,275 HelpFormatter - ----------------------------------------------------------------------------------
INFO 13:02:12,275 HelpFormatter - ----------------------------------------------------------------------------------
INFO 13:02:12,496 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:02:12,813 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:02:13,584 PedReader - Reading PED file /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped with missing fields: []
INFO 13:02:13,599 PedReader - Phenotype is other? false
INFO 13:02:13,882 GenomeAnalysisEngine - Preparing for traversal
INFO 13:02:13,890 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:02:13,890 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:02:13,890 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:02:13,891 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

ERROR --
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 2
at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.getLikelihoodsAsMapSafeNull(FamilyLikelihoodsUtils.java:455)
at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.updateFamilyGenotypes(FamilyLikelihoodsUtils.java:392)
at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.calculatePosteriorGLs(FamilyLikelihoodsUtils.java:263)
at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:345)
at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:189)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.broadinstitute.org/gatk

Is this caused by the liftover or it's a different issue? Any idea how to fix this?

Cheers,

Steph

Post edited by shlee on

Best Answer

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @sbourgeois,

    Looks like LiftoverVcf is getting some attention these days. What version of Picard are you using? It seems there was a release (v2.10.2) not six hours ago that fixes a LiftoverVcf bug.

  • sbourgeoissbourgeois London, UKMember

    Hi @shlee

    I used 2.10.0, which was the latest version. I will try 2.10.2 and report back, thanks.

    Steph

  • sbourgeoissbourgeois London, UKMember

    Hi @shlee

    liftover using Picard 2.10.2 completed and I resubmitted my job, with the same result unfortunately:

    OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
    OpenJDK 64-Bit Server VM warning: If the number of processors is expected to increase from one, then you should configure the number of parallel GC threads appropriately using -XX:ParallelGCThreads=N
    INFO 11:04:58,201 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 11:04:58,224 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
    INFO 11:04:58,228 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
    INFO 11:04:58,234 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
    INFO 11:04:58,234 HelpFormatter - [Fri Jul 14 11:04:58 BST 2017] Executing on Linux 3.10.0-514.16.1.el7.x86_64 amd64
    INFO 11:04:58,236 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_131-b12
    INFO 11:04:58,240 HelpFormatter - Program Args: -T CalculateGenotypePosteriors -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -V /data/WHRI-Panos-Scratch/hhx037/piperi/filtered/piperi_snps_indels.vcf --supporting /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.sites.vcf -ped /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped -o ./refined/piperi_snps_indels.postCGP.vcf
    INFO 11:04:58,271 HelpFormatter - Executing as hhx037@dn26 on Linux 3.10.0-514.16.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b12.
    INFO 11:04:58,272 HelpFormatter - Date/Time: 2017/07/14 11:04:58
    INFO 11:04:58,273 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 11:04:58,273 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 11:04:58,501 GenomeAnalysisEngine - Strictness is SILENT
    INFO 11:04:58,941 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    INFO 11:04:59,955 PedReader - Reading PED file /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped with missing fields: []
    INFO 11:04:59,971 PedReader - Phenotype is other? false
    INFO 11:05:00,519 GenomeAnalysisEngine - Preparing for traversal
    INFO 11:05:00,536 GenomeAnalysisEngine - Done preparing for traversal
    INFO 11:05:00,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 11:05:00,552 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 11:05:00,552 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

    ERROR --
    ERROR stack trace

    java.lang.ArrayIndexOutOfBoundsException: 2
    at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.getLikelihoodsAsMapSafeNull(FamilyLikelihoodsUtils.java:455)
    at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.updateFamilyGenotypes(FamilyLikelihoodsUtils.java:392)
    at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.calculatePosteriorGLs(FamilyLikelihoodsUtils.java:263)
    at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:345)
    at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:189)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
    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 https://software.broadinstitute.org/gatk

    So, I decided to test using 1000G_phase1.snps.high_confidence.hg19.sites.vcf which is part of the hg19 bundle and doesn't have to get lifted, and again:

    OpenJDK 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
    OpenJDK 64-Bit Server VM warning: If the number of processors is expected to increase from one, then you should configure the number of parallel GC threads appropriately using -XX:ParallelGCThreads=N
    INFO 11:15:26,826 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 11:15:26,865 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
    INFO 11:15:26,865 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
    INFO 11:15:26,865 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
    INFO 11:15:26,865 HelpFormatter - [Fri Jul 14 11:15:26 BST 2017] Executing on Linux 3.10.0-514.16.1.el7.x86_64 amd64
    INFO 11:15:26,865 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_131-b12
    INFO 11:15:26,870 HelpFormatter - Program Args: -T CalculateGenotypePosteriors -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -V /data/WHRI-Panos-Scratch/hhx037/piperi/filtered/piperi_snps_indels.vcf --supporting /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf -ped /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped -o ./refined/piperi_snps_indels.postCGP.vcf
    INFO 11:15:26,895 HelpFormatter - Executing as hhx037@dn22 on Linux 3.10.0-514.16.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_131-b12.
    INFO 11:15:26,896 HelpFormatter - Date/Time: 2017/07/14 11:15:26
    INFO 11:15:26,896 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 11:15:26,896 HelpFormatter - ----------------------------------------------------------------------------------
    INFO 11:15:27,064 GenomeAnalysisEngine - Strictness is SILENT
    INFO 11:15:27,471 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
    WARN 11:15:29,117 RMDTrackBuilder - Index file /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx is out of date (index older than input file), deleting and updating the index file
    INFO 11:20:21,283 RMDTrackBuilder - Writing Tribble index to disk for file /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx
    INFO 11:21:13,158 PedReader - Reading PED file /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped with missing fields: []
    INFO 11:21:13,194 PedReader - Phenotype is other? false
    INFO 11:21:13,490 GenomeAnalysisEngine - Preparing for traversal
    INFO 11:21:13,524 GenomeAnalysisEngine - Done preparing for traversal
    INFO 11:21:13,525 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
    INFO 11:21:13,527 ProgressMeter - | processed | time | per 1M | | total | remaining
    INFO 11:21:13,528 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime

    ERROR --
    ERROR stack trace

    java.lang.ArrayIndexOutOfBoundsException: 2
    at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.getLikelihoodsAsMapSafeNull(FamilyLikelihoodsUtils.java:455)
    at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.updateFamilyGenotypes(FamilyLikelihoodsUtils.java:392)
    at org.broadinstitute.gatk.tools.walkers.variantutils.FamilyLikelihoodsUtils.calculatePosteriorGLs(FamilyLikelihoodsUtils.java:263)
    at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:345)
    at org.broadinstitute.gatk.tools.walkers.variantutils.CalculateGenotypePosteriors.map(CalculateGenotypePosteriors.java:189)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
    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 https://software.broadinstitute.org/gatk
    ERROR

    So, as it crashes even when using an original hg19 file from the bundle, the error I encounter may not be linked to the liftover after all. Any other test I can do? Any idea of what's causing this?

    Cheers,

    Steph

    Issue · Github
    by shlee

    Issue Number
    2289
    State
    closed
    Last Updated
    Assignee
    Array
    Closed By
    chandrans
  • shleeshlee CambridgeMember, Broadie, Moderator

    Steph (@sbourgeois),

    So we've ruled out the liftover code changes as a source of error. I'm not familiar with CalculateGenotypePosteriors and so let me get someone who is to look into the error.

  • ronlevineronlevine Lexington, MAMember

    @sbourgeois After looking at the call stack, the error is due to one of the VCF samples from the mother, father or child having 2 instead of 3 items for PP or PL. Since 1000G_phase1.snps.high_confidence.hg19.sites.vcf does not contain genotypes, this should not be possible. What is your command line for CalculateGenotypePosteriors?

  • sbourgeoissbourgeois London, UKMember

    Hi @ronlevine

    thanks for looking into this.

    As per the trace posted, the command used was -T CalculateGenotypePosteriors -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -V /data/WHRI-Panos-Scratch/hhx037/piperi/filtered/piperi_snps_indels.vcf --supporting /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/1000G_phase3_v4_20130502.hg19.sites.vcf -ped /data/WHRI-Panos-Scratch/hhx037/piperi/piperi.ped -o ./refined/piperi_snps_indels.postCGP.vcf

    Before that, samples were called individually (in gvcf format) using commands such as:
    -T HaplotypeCaller -ploidy 2 -L female.list -nct 1 -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -I /data/WHRI-Panos-Scratch/hhx037/piperi/recalibrated/mother.bam --genotyping_mode DISCOVERY --emitRefConfidence GVCF -o ./variants/mother.g.vcf --dbsnp /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/dbsnp_138.hg19.vcf -bamout ./haplotypes/mother.haplotypes.bam -L /data/WHRI-Panos-Scratch/hhx037/piperi/GC-SB-6507_NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.bed -ip 100

    and for X and Y for males:
    -T HaplotypeCaller -ploidy 1 -L XY.list -nct 1 -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -I /data/WHRI-Panos-Scratch/hhx037/piperi/recalibrated/father.bam --genotyping_mode DISCOVERY --emitRefConfidence GVCF -o ./variants/father.XY.g.vcf --dbsnp /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/dbsnp_138.hg19.vcf -bamout ./haplotypes/father.haplotypes.XY.bam -L /data/WHRI-Panos-Scratch/hhx037/piperi/GC-SB-6507_NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.bed -ip 100

    and then all gvcfs were called together using: -T GenotypeGVCFs -nt 2 -R /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/ucsc.hg19.fasta -o ./joint_genotype/piperi.vcf --dbsnp /data/WHRI-Panos-Scratch/REPOSITORY/GATK_resources/hg19/dbsnp_138.hg19.vcf --variant ./variants/father.g.vcf --variant ./variants/father.XY.g.vcf --variant ./variants/mother.g.vcf --variant ./variants/son.g.vcf --variant ./variants/son.XY.g.vcf

    Cheers

  • ronlevineronlevine Lexington, MAMember

    @sbourgeois Does piperi_snps_indels.vcf have any samples with 2 instead of 3 PL values? I noticed for X and Y for males, HaplotypeCaller uses -ploidy 1 with human sequence data. GenotypeGVCFs will output a mixed ploidy VCF.

  • sbourgeoissbourgeois London, UKMember

    @ronlevine The number of PL values seem to vary from one variant to the other:

    chrM 16528 . G A 1452.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-7.820e-01;ClippingRankSum=0.00;DP=151;ExcessHet=3.9794;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=59.32;MQRankSum=-5.660e-01;QD=12.52;ReadPosRankSum=0.629;SOR=0.629 GT:AD:DP:GQ:PGT:PID:PL 0/0:29,0:29:87:.:.:0,87,697 0/1:55,34:89:99:.:.:551,0,2216 0/1:3,24:27:48:0|1:16521_C_T:933,0,48

    chr1 13273 . G C 1226.35 . AC=3;AF=0.500;AN=6;BaseQRankSum=0.790;ClippingRankSum=0.00;DP=272;ExcessHet=3.0103;FS=1.908;MLEAC=3;MLEAF=0.500;MQ=41.76;MQRankSum=1.10;QD=6.59;ReadPosRankSum=2.07;SOR=0.537 GT:AD:DP:GQ:PL 1:26,43:69:99:268,0 0/1:16,32:48:99:726,0,255 0:7,0:7:99:0,135

    chr1 866319 rs9988021 G A 347.44 . AC=6;AF=1.00;AN=6;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;QD=28.95;SOR=3.611 GT:AD:DP:GQ:PL 1:0,2:2:48:48,0 1/1:0,4:4:12:127,12,0 1:0,2:2:75:75,0

    chr1 866893 rs2880024 T C 73.17 . AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=18.29;SOR=0.693 GT:AD:DP:GQ:PL ./.:0,0:0:.:0,0,0 1/1:0,4:4:12:99,12,0 ./.:0,0:0:.:0,0,0

    I'm not sure what to do.

  • sbourgeoissbourgeois London, UKMember

    @Geraldine_VdAuwera OK, it makes sense now... thanks a lot, I'll rerun HCaller

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