[Bioperl-l] Getting pileup consensus from BAM files using Bio::DB::Sam

Lincoln Stein lincoln.stein at gmail.com
Tue Aug 3 12:57:52 EDT 2010


Samtools is running MAQ on the pileup. You could either implement MAQ in
perl, or come up with your own consensus caller.

Lincoln

On Tue, Aug 3, 2010 at 1:29 AM, Gowthaman Ramasamy <
gowthaman.ramasamy at seattlebiomed.org> wrote:

> Hi List,
> I am trying to find out the consensus using pileup via Bio::DB::Sam. Using
> the following script I could parse out the ref_base and different bases from
> reads at that position. Though, I am not able to find a method to derive
> consensus. Similar to the values produced by "samtools pileup -c -f
> xxxxxx.fasta yyyyyyy.bam".
>
> The script I use now retrives ref base, query bases for each position. How
> do I improve it to get the consensus?
>
> Thanks very much in advance,
> Gowthaman
>
>
> use Bio::DB::Sam;
>
> my $bam = Bio::DB::Sam->new(-bam => 'something.bam',
>                            -fasta => 'something.fasta'
>                           );
>
> my $cb = sub {
>                        my ($seqid, $pos, $pileups) = @_;
>                        my $refBase = $bam->segment($seqid, $pos,
> $pos)->dna;
>                        print "\n$pos\t$refBase=>";
>                        for my $pileup (@$pileups){
>                                my $al = $pileup->alignment;
>                                my $qBase = substr($al->qseq, $pileup->qpos,
> 1);
>                                print "$qBase,";
>                                }
>                        };
>
> $bam->pileup('Lin.chr10i', $cb);
>
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>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>


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