get read position from Samtools pileup

[rcorbett]

Hi all,
Has anyone come across a way to get information about the location of a snp within the reads? I have the usual bam/sam/pileup files.

For example,
r1: GAG
r2: GGG
r3: AGA
ref: AAAGGGTTTT

In this very contrived example that was hopefully preserved by the editor we would have a single snp represented at pos 2 in read 1, and pos 3 in read 3 . What I am looking for is a way to get that information that says this snp is at pos 2 in r1, and position 3 in r3 from bam/sam/pileup files.

Does anyone know of a tool that can do this?

thanks for any help.

[rcorbett]

Hmm. The editor ate the example.
I'll use '#' to mark spaces:

r1: ###GAG###
r2: ###GGG###
r3: ##AGA####
rf: AAAGGGTTTT

[krobison]

Probably not the answer you were looking for, but you could certainly roll your own using one of the SAMTools libraries for Perl, Python or Java. The Perl SNP caller example shows this:

http://search.cpan.org/~lds/Bio-SamTools-1.05/lib/Bio/DB/Sam.pm#Examples

(I've added some additional comments; the code is not mine)

 my @SNPs;  # this will be list of SNPs
 my $snp_caller = sub {
        my ($seqid,$pos,$p) = @_;
        my $refbase = $sam->segment($seqid,$pos,$pos)->dna;
        my ($total,$different);
        for my $pileup (@$p) {
            my $b     = $pileup->b;
            next if $pileup->indel;  # don't deal with these ;-)

            # $pileup->qpos is the position in $b->qseq (the read)
            my $qbase  = substr($b->qseq,$pileup->qpos,1);
            next if $qbase =~ /[nN]/;

            my $qscore = substr($b->qscore,$pileup->qpos,1);
            next unless $qscore > 25;

            $total++;
           # next line finds the variant; 
            $different++ if $refbase ne $qbase;
        }
        if ($total >= 4 && $different/$total >= 0.25) {
           push @SNPs,"$seqid:$pos";
        }
    };

 $sam->pileup('seq1',$snp_caller);
 print "Found SNPs: @SNPs\n";