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Old 07-09-2010, 04:06 AM   #2
Dethecor
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Location: Germany

Join Date: May 2010
Posts: 24
Default Have a look at the samtools pileup format

See here: http://samtools.sourceforge.net/pileup.shtml

also, if you run samtools with the following command "samtools pileup -c -f <reference_sequence> in.bam" you will get for each position the support for consensus and for reference and some value that tells you the probability of a SNP at this position, I haven't read up on the details but I think that could be a good starting point.

Example Output:

dmel_mitochondrion_genome 2033 T T 10 0 0 3 ... AA>


You could try to extract your desired information from that.

Cheers,
Paul
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