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GenotypeGVCFs variant IDs
I am trying to use GenotypeGVCFs to perform joint genotyping on 16 samples. These 16 samples were sequenced twice on two different machines, so I actually have 32 readsets. I called variants for each using HaplotypeCaller, producing GVCFs and am now trying to combine these into a single multi-sample VCF, wherein the resultant multisample file will contain information for all variant loci across the cohort. However, since the samples have the same names, when I try to use GenotypeGVCFs, they are seemingly collapsed, so I only have 16 samples recorded in my output VCF. I tried specifying variant names in the format --variant:name input1.g.vcf with both GenotypeGVCFs and CombineGVCFs but had the same result - half the samples missing in the output. I know it is possible to do this using CombineVariants, but this will not take GVCF input. Is it possible to specify names for the variants when using GenotypeGVCFs?
I appreciate your help, many thanks in advance.