Entering edit mode
6.0 years ago
mluypaert
▴
10
Hi All
I was look at the samtools mpileup output format and found something odd in the reported quality scores.
1 633887 G 28 >><<<<CAAA.AA.AAAcaAAAC.A..a E//E/E6i/EiEEEEEE//AEE//EEEA
In the line above, some calls get a (phred+33 I assume) quality i. As I understand pileup format description (http://samtools.sourceforge.net/pileup.shtml), this should be the mapping quality of the reads at that base. However, when I look at the mapped reads at that position in the .bam file (using samtools view), I find no i quality scores anywhere near those positions.
Hence the question: what quality scores are reported by samtools mpileup?
