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Snps Calling With Samtools

Hi All,

I''ve created .bam file with Bowtie2. I want to use samtools for SNP calling . but I couldn't find command to do this task. could somebody help me ?

ngs
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updated by aawitney • aawitney • written by jack • jack

I would recommend Genome Analysis Toolkit (GATK) for snp calling than samtools.

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written by samsara samsara

2 answers

People been posting their pipelines on biostar

Another suggestion is to use search program/tool on github - there are many commands with various samtools options.

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updated by Istvan Albert Istvan Albert • written by PoGibas PoGibas

The samtools manual page gives a good starting point:

http://samtools.sourceforge.net/mpileup.shtml

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written by aawitney • aawitney

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