Dear all,
I am very confused by what I am getting from samtools mpileup: the selection of a specific region completely changes the output.
Precisely if I run this:
$samtools mpileup -q 20 -r 1:110754254-110754254 -f $fasta -sO $bam
The the base qualities are very low:
1 110754254 A 2 GG %% [V 18,18
But if I run:
$samtools mpileup -q 20 -f $fasta -sO $bam | grep 110754254
Then the base qualities become much higher:
1 110754254 A 2 GG GG [V 18,18
What is going on here?
Help welcome,
Update: some progress: it looks like the issue is that if I don't specify the -r flag, samtools does not use BAQ computation. But why wouldn't samtools turn BAQ computation off if a region is not specified? If I disable BAQ computation in the region specific mpileup then the qualities become consistent. This is really odd.
Vincent
I am very confused by what I am getting from samtools mpileup: the selection of a specific region completely changes the output.
Precisely if I run this:
$samtools mpileup -q 20 -r 1:110754254-110754254 -f $fasta -sO $bam
The the base qualities are very low:
1 110754254 A 2 GG %% [V 18,18
But if I run:
$samtools mpileup -q 20 -f $fasta -sO $bam | grep 110754254
Then the base qualities become much higher:
1 110754254 A 2 GG GG [V 18,18
What is going on here?
Help welcome,
Update: some progress: it looks like the issue is that if I don't specify the -r flag, samtools does not use BAQ computation. But why wouldn't samtools turn BAQ computation off if a region is not specified? If I disable BAQ computation in the region specific mpileup then the qualities become consistent. This is really odd.
Vincent