Re: [Samtools-help] retrieving base frequencies at specific position

[Ryan G. <ngs...@gm...>]

I have a java program that does exactly this.  I'll email you off list with
the program.



On Tue, Jan 29, 2013 at 12:42 PM, Hanspeter Niederstrasser <
fi...@sn...> wrote:

> I have a set of 86 aligned bam files from an Illumina targeted
> resequencing run.  Because the input samples were not clonal, we are
> interested in determining the frequency of bases at each position along
> the sequenced amplicon (~3kb).
>
> Basically, at the end of the day, I want to be able to generate a table
> that conceptually looks like this (pos 1 had 13 reads in the bam: 6 C
> and 7 T):
>
> Pos A C T G
> 1   0 6 7 0
> 2   0 0 0 12
> 3  10 1 1 0
> ...
>
> Parsing the Illumina provided VCF files doesn't give me the coverage
> that I need since many of the variants are of low frequency (< 5%) and
> many positions have more than one variant.  The closest I've been able
> to get is to modify this script <http://www.biostars.org/p/45384/> to
> work with mpileup output, and that gives me output like this:
>
> 311     A 40
> 312     T 39    C 1
> 313     C 29    T 7
>
> but when I look at my .bam file in IGViewer, the number of reads
> actually present is about 2.5 times higher than what the script presents
> (eg 86 reads for position 313).
>
> Is there some software solution that already exists that would allow me
> individually read and tally bases along a bam? Or can someone point out
> why the above script is not giving the accurate counts for each position
> from the mpileup output?
>
> Thanks,
>
> Hanspeter
>
>
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