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Dethecor · 07-09-2010, 04:06 AM

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

07-09-2010, 04:06 AM	#2
Dethecor Member Location: Germany Join Date: May 2010 Posts: 24	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