Question: What is ploidy level for HaplotypeCaller ?
0
gravatar for mirzaei86.vahid
24 months ago by
mirzaei86.vahid30 wrote:

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

snp gatk genome • 882 views
ADD COMMENTlink modified 24 months ago by WouterDeCoster38k • written 24 months ago by mirzaei86.vahid30
0
gravatar for WouterDeCoster
24 months ago by
Belgium
WouterDeCoster38k wrote:

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

ADD COMMENTlink written 24 months ago by WouterDeCoster38k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1955 users visited in the last hour