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  • ACGT counts from mpileup

    I would like to get the counts of A/C/G/T high quality bases aligned at each position from a bam file.

    I know that 'samtools mpileup' gives a string with actual read bases and their quality scores ("reads" and "quals" in example below). So, yes I can parse it. But is there a ready-made option for this?

    Code:
    Chr      pos     Ref     Dep    Reads     Quals
    1	3000016	A	5	..C.^~.	/<%A?
    I also know that the '-u' option gives something similar in the I16 filed (number of bases in forward and reverse strand which are ref or non-ref) but not quite the full A/C/G/T count.

    So, is parsing each mpileup line my only option? (Are there other programs, say picard, which might be better suited for this?)

    Thanks,
    Gulu
    Last edited by kgulukota; 04-27-2012, 06:23 AM.
    Kamalakar Gulukota,
    Director,
    Center for Bioinformatics and Computational Biology
    NorthShore University Health System, [email protected]

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