how to find somatic variant with single bam file by samtools ?

Question

[Anop Singh Ranawat]

thanks in advance how to find somatic variant with single bam file by samtools ?

hii i have one bam file and i want to call somatic variant by samtools. what will be command ?

Answer 1

[Devon Ryan]

Here is the workflow suggested by the samtools folks for variant calling. You'll note that this is not specifically for somatic variant calls, since the samtools suite is a more generic variant caller.

[Anop Singh Ranawat]

thanks , but is there any open source somatic caller ?

[Devon Ryan]

FreeBayes and mutect come to mind.