MergeVcfs vs GatherVCFs in GATK 4
0
0
Entering edit mode
3.5 years ago
MAPK ★ 2.1k

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 • 1.9k views
ADD COMMENT

Login before adding your answer.

Traffic: 2909 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6