Is HaplotypeCaller a softwar for SNP and Indel calling in GATK just for haploid cell? Can we use it for somatic cells?

Seyed Morteza Razavi @Seyed-Morteza-Razavi

08 November 2017 1 8K Report

I have applied my SAM file from somatic exome data on HaplotypeCaller software and it has generate a VCF file contain multiple SNPs and Indels.

Is this software just for haploid cells?

Snijesh V.P.

Hi Seyed,

GATK HaplotypeCaller is designed to call germline mutation from the samples. It is not good idea to use it in your analysis to call somatic mutation.

There is another package Mutect2 specially designed to capture somatic mutation

https://software.broadinstitute.org/gatk/best-practices/mutect2.php

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