Snps Calling With Samtools
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10.7 years ago
jack ▴ 520

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 • 3.1k views
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I would recommend Genome Analysis Toolkit (GATK) for snp calling than samtools.

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10.7 years ago
PoGibas 5.1k

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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10.7 years ago
aawitney ▴ 20

The samtools manual page gives a good starting point:

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

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