what is the best order to use HC, GenotypeVCFs, VariantRecalibrate and CombineVariants?

Hi all,
I have 2 DNAseq batches of samples (more batches are ongoing sequencing, i.e. cohort). I used HaplotypeCaller per sample and got 2 batches of gvcfs, one gvcf per sample. But I am not sure which of the following order is best: (CombineGVCFs per batch) -> GenotypeGVCFs (obtain a single vcf) -> VariantRecalibration, or GenotypeGVCFs per batch -> VariantRecalibration per batch -> CombineVariant (obtain a single vcf). What is the difference between these two orders? and which one is more suitable for my situation? Hoping for any suggestions. Thank you very much !

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    Hi Hiu,

    It is better to run Haplotype Caller, CombineGVCFs, GenotypeGVCFs, and VQSR. The more variants you have for VQSR, the better.

    However, you only need to run Combine GVCFs if you have batches greater than 200. If less than 200, you can simply run GenotypeGVCFs.


  • zuoxyzuoxy ChinaMember

    Thanks Sheila. But I further want to figure out whether there is any difference on the final vcf between the two workflow: GenotypeGVCFs all samples together then VQSR and GenotypeGVCFs+VQSR per batch then CombineVariants. Does GATK have some worker to compare the two vcfs? e.g. genotypeConcordance, but could output more detail about the disconcordance.


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