MergeVcfs vs GatherVCFs in GATK 4
Hi All,
I am using GATK after several years. I used to merge chromosomes chr{1..22} chrX and chrY with same samples using catVariants in GATK3. It looks like they have replaced this tool with something different on GATK4. So I would like to confirm if I am using right tools-
- Do I use GatherVcfs to consolidate all chromosomes?
- If I need to merge two VCFs with different samples, do I use MergeVCFs?
TIA
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