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From BAM/SAM to number of A,C,G,T at each location

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  • dgscofield
    replied
    I wrote a little Perl script to generate an mlRho profile file from samtools mpileup. You can find pileup2pro.pl at https://github.com/douglasgscofield/...master/scripts. Bernhard also links to it from the mlRho site.
    Last edited by dgscofield; 08-07-2012, 08:42 AM.

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  • donniemarco
    replied
    (I would like to obtain the number of A,C,G and T at each position of each contig from a SAM/BAM file.)

    I think GATK tools does that. I am also using it to calculate the breakdown of each nucleotide at every position matching reference.

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  • Sylphide
    replied
    The author Bernhard Haubold created a script to go from SAMTOOLS pileup to number of A,T,C,G available on asking.

    Thanks for your help mgogol anyway

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  • mgogol
    replied
    One way I know of is to run samtools mpileup, but you'll have to write another script to interpret and format the output.

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  • From BAM/SAM to number of A,C,G,T at each location

    Hi,
    I would like to obtain the number of A,C,G and T at each position of each contig from a SAM/BAM file.

    This is tu run the program mlRho from Bernhard Haubold, Peter Pfaffelhuber and Michael Lynch (http://guanine.evolbio.mpg.de/cgi-bi...o/mlRho.cgi.pl).
    The program can also use ACE format but I don't know how to obtain ACE from BAM.

    I don't know if there already is some tool available to do that, otherwise I will have to code it myself.

    Many thanks in advance for your help
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