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Old 07-08-2010, 01:48 PM   #1
Lee Sam
Location: Ann Arbor, MI

Join Date: Oct 2008
Posts: 57
Default Supporting Reads in SAMTools SNP Calls

I'm using SAMTools to do some variant calling and I'd like to know how many supporting reads there are for the variant vs the consensus for the SNPs that it calls (like the indel lines). Is there a way to do this that I've missed? I want to use it as a filter on top of the mapping qualities.
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Old 07-09-2010, 03:06 AM   #2
Location: Germany

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

See here:

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.

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Old 07-09-2010, 06:16 AM   #3
Lee Sam
Location: Ann Arbor, MI

Join Date: Oct 2008
Posts: 57

Got it, thanks. I'll parse the read base column.
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