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

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 ?

next-gen • 1.6k views
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4.2 years ago

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.

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thanks , but is there any open source somatic caller ?

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FreeBayes and mutect come to mind.

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