Joint variant calling on DeepVariant GVCFs using GATK GenotypeGVCFs · Biostar

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Joint variant calling on DeepVariant GVCFs using GATK GenotypeGVCFs

Hi everyone I have a bunch of GVCF files generated by DeepVariant, but I want to use GATK's GenotypeGVCFs for joint variant calling on them (I don't want to use GLnexus). But GATK requires a genotype likelihood field produced by its HaplotypeCaller. Is there any way to make my GVCFs compatible with GATK?

P.S. Are there any other solid tools besides GATK and GLnexux for joint variant calling on GVCFs?

genotypegvcfs joint calling variant gatk gvcf deepvariant

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written 4.0 years ago by Matin •

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