Snps Calling With Samtools

Question

[jack]

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 ?

[samsara]

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

Answer 1

[PoGibas]

People been posting their pipelines on biostar

• Genomic Alignment and SNP/Indel Calling - My first ever "Pipeline"
• What is the best pipeline for human whole exome sequencing?

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

Answer 2

[aawitney]

The samtools manual page gives a good starting point:

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