What is ploidy level for HaplotypeCaller ?
1
0
Entering edit mode
4.8 years ago

Dear all,

I have rudimentary questions about GATK pipline:

First about HaplotypeCaller , I have set -ploidy 1 , my sample belong to human specie.

Is it correct to set ploidy=1 for human?

I'm working on germline mutation but I saw different pipeline for somatic mutation in GATK best practice,I'd like to know for finding somatic mutation we should have at least >=2 samples to make comparison right?

And What is the best tool in GATK for somatic mutation?

Regards, Vahid

GATK SNP genome • 1.8k views
ADD COMMENT
0
Entering edit mode
4.8 years ago

Humans are diploid, so ploidy = 2, which is the default setting so you don't have to specify this.

ADD COMMENT

Login before adding your answer.

Traffic: 2916 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