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HaplotypeCaller and GenotypeGVCF

AswathyNAswathyN BangaloreMember

I am performing variant calling on Targetted Exome Samples (TES) (Human) using licensed version of GATK (V2014.3-3.2.2-7-g f9cba99)
My samples are amplicon based targetted sequences.
Currently I perform Haplotype calling for individual TES and then Genotype GVCF step for the samples together. My question is :
1) Is it fine to do Haplotype calling and Genotype GVCF steps for all the TES samples together, rather than doing Haplotype calling for individual samples and Genotype GVCF step for the samples together, as mentioned above.




  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Aswathy,

    I am not sure I understand your question. You should use Haplotype Caller to get a GVCF for each sample, then run GenotypeGVCFs on all the individual GVCFs to get a multi-sample VCF. You cannot run Haplotype Caller in GVCF mode on many samples together. Haplotype Caller in GVCF mode accepts only one sample at a time.


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