CombineGVCFs vs. MergeVcfs

Question

[Sd]

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?

Answer 1

[Pierre Lindenbaum]

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

[Jeremy Leipzig]

in the supplemental materials of that UKBB paper they actually do mention MergeVcfs but it must be a typo