Somatic Variant Calling

Question

[adarsh_munna]

Hi,

I need to call somatic variants from a BAM file of cancer panel.

Can anyone please suggest any suitable tool for calling the variants and generate a VCF file.

Thank You

Answer 1

[aldhairmedico]

"Suitable" is very context-dependent, are you working with WGS or WES data? short o long reads? Check the Mutect2 pipelines from GATK and you must look for other variant callers in the literature.

[adarsh_munna]

It is an Ampliseq sequencing with custom bed file

Answer 2

[ATpoint]

https://github.com/nf-core/sarek

Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with Docker containers making installation trivial and results highly reproducible.