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Old 05-17-2011, 12:16 PM   #1
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Default listing specific reads with SNP using samtools

Is it possible using the out of the box samtools to list what reads (read IDs) were used in determining a specific SNP call? Poking around it seems like it might be possible using the BioPerl or pysam libraries but was wondering if the samtools binary could maybe do this when using pileup or mpileup.

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samtools, samtools pileup

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