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

[Sylphide]

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

[mgogol]

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

[Sylphide]

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

[donniemarco]

(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.

[dgscofield]

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.