Question: MergeVcfs vs GatherVCFs in GATK 4
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gravatar for MAPK
6 weeks ago by
MAPK1.7k
MAPK1.7k wrote:

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-

  1. Do I use GatherVcfs to consolidate all chromosomes?
  2. If I need to merge two VCFs with different samples, do I use MergeVCFs?

TIA

gatk • 166 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by MAPK1.7k
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