Hello,
I work on merging GVCF files. Each sample has undergone HaplotypeCaller, and GVCF files were created by chromosome. Now, I have 24 GVCF files per sample and I want to merge them into a single GVCF file per sample. Eventually, I am going to use GVCF files in GenomicsDBImport and then do GenotypeGVCFs for joint calling.
To merge GVCFs, some papers have done this by using MergeVcfs (as in https://www.nature.com/articles/s41586-022-04965-x) and some resources recommend CombineGVCFs. What is the efficient way to merge GVCFs: using CombineGVCFs or MergeVcfs?
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CombineGVCFs : is used to combine GGGGGGGGGGGGGGGGGGGGGGGGvcfs files . See https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-VCF-Genomic-Variant-Call-Format
while MergeVcfs is only used to combine VCF files.
So if you generated GVCF, you'll need CombineGVCFs followsed by GenotypeGVCFs
in the supplemental materials of that UKBB paper they actually do mention MergeVcfs but it must be a typo
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