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Old 06-21-2011, 06:11 AM   #1
Sylphide
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Default 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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Old 06-21-2011, 07:02 AM   #2
mgogol
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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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Old 06-22-2011, 05:30 AM   #3
Sylphide
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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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Old 06-22-2011, 09:56 AM   #4
donniemarco
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(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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Old 08-07-2012, 09:39 AM   #5
dgscofield
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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.

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