Hello everyone,
I'm running mpileup twice on the same BAM alignment of RNASeq reads against the same reference genome, with and without filtering for mapping quality (-q 5 or not), and getting, (I think) an odd result.
I checked the same position on the same chromosome between the filtered and unfiltered output.
In both cases, 7997 reads overlapped that position, but the counts of reads that matched the reference (,.) versus those that were mismatches (Aa) was drastically different between the two. Specifically, there were far more mismatches at that position in the filtered output than in the unfiltered output.
If I'm understanding what -q does correctly, it should simply be disregarding alignments with a mapq score of lower than 5 (if I use -q 5), right? So I would understand if the number of reads overlapping the position was reduced, but I don't understand why the count of overlapping reads would remain the same, but the proportion of matches to mismatches would change.
Can anyone help me make sense of this?
Thanks,
Alex
P.S.
samtools 0.1.18
Linux OS
I'm running mpileup twice on the same BAM alignment of RNASeq reads against the same reference genome, with and without filtering for mapping quality (-q 5 or not), and getting, (I think) an odd result.
I checked the same position on the same chromosome between the filtered and unfiltered output.
In both cases, 7997 reads overlapped that position, but the counts of reads that matched the reference (,.) versus those that were mismatches (Aa) was drastically different between the two. Specifically, there were far more mismatches at that position in the filtered output than in the unfiltered output.
If I'm understanding what -q does correctly, it should simply be disregarding alignments with a mapq score of lower than 5 (if I use -q 5), right? So I would understand if the number of reads overlapping the position was reduced, but I don't understand why the count of overlapping reads would remain the same, but the proportion of matches to mismatches would change.
Can anyone help me make sense of this?
Thanks,
Alex
P.S.
samtools 0.1.18
Linux OS
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