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SampleList annotation returns only one sample while being used in a variant call on two samples

ArvandArvand IranMember

Hi there,

I have used HaplotypeCaller from GATK4 to call variants on two affected siblings. I put SampleList annotation in the command but only one sample is seen in all of the variants in the resulting VCF file.
Mind you I have done this before on GATK 3x versions and never had such a problem. I could use the "set" column to see variants regarding each sample easily.

gatk HaplotypeCaller \ -R ~/Arvand/hg19/ucsc.hg19.fasta \ -I ~/Arvand/5137D_recalibrated.bam \ -I ~/Arvand/5137E_recalibrated.bam -O affected_raw.vcf.gz \ -bamout affected_bamout.bam -A BaseQuality -A ChromosomeCounts -A Coverage -A DepthPerAlleleBySample -A RMSMappingQuality -A OxoGReadCounts -A QualByDepth -A FisherStrand -A StrandOddsRatio -A SampleList --genotyping-mode DISCOVERY -D ~/Arvand/hg19/dbsnp_147.hg19.vcf.gz --native-pair-hmm-threads 20


Best Answer


  • ArvandArvand IranMember

    Hi @Sheila ,

    I know you are very busy with the forum and I am sorry to bother you but do you have any idea what might have gone wrong with my command?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I just tested this with version, and the SampleList annotation works for me. Can you post some example records that only show one sample?


  • ArvandArvand IranMember
    edited March 7


    Unfortunately no. I deleted those files due to lack of free space and started everything from scratch triple-checking every command and validating files at every step. If I encounter the problem again I will get back to you here.

  • ArvandArvand IranMember
    Accepted Answer


    sample list seems to be in order now. I think I should have made a mistake at defining read groups while mapping and it dragged on till the end.

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