Hi All,
samtools mpileup has a -Q option which "skip bases with baseQ/BAQ smaller than INT [13]". My understanding is that bases with phred quality (11th column in SAM) less than Q are not counted in the resulting pileup, right?
However, it seems to me that -Q has no effect. Here's an example using the toy.sam file in the example dir that comes with samtools:
I'm using samtools 0.1.15. Am I missing something obvious here?
All the best
Dario
samtools mpileup has a -Q option which "skip bases with baseQ/BAQ smaller than INT [13]". My understanding is that bases with phred quality (11th column in SAM) less than Q are not counted in the resulting pileup, right?
However, it seems to me that -Q has no effect. Here's an example using the toy.sam file in the example dir that comes with samtools:
Code:
## Convert SAM to BAM samtools view -b -S /.../samtools-0.1.15/examples/toy.sam > toy.bam samtools view toy.bam r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA * r003 0 ref 9 30 5H6M * 0 0 AGCTAA * r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC * r003 16 ref 29 30 6H5M * 0 0 TAGGC * r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * x1 0 ref2 1 30 20M * 0 0 AGGTTTTATAAAACAAATAA ???????????????????? x2 0 ref2 2 30 21M * 0 0 GGTTTTATAAAACAAATAATT ????????????????????? x3 0 ref2 6 30 9M4I13M * 0 0 TTATAAAACAAATAATTAAGTCTACA ?????????????????????????? x4 0 ref2 10 30 25M * 0 0 CAAATAATTAAGTCTACAGAGCAAC ????????????????????????? x5 0 ref2 12 30 24M * 0 0 AATAATTAAGTCTACAGAGCAACT ???????????????????????? x6 0 ref2 14 30 23M * 0 0 TAATTAAGTCTACAGAGCAACTA ??????????????????????? ## Produce pileup: samtools mpileup toy.bam > toy.mpileup ## Produce pileup with ridiculously high -Q: samtools mpileup -Q 100 toy.bam > toyQ.mpileup ## -Q has no effect! wc toy.mpileup toyQ.mpileup 75 450 1473 toy.mpileup 75 450 1473 toyQ.mpileup 150 900 2946 total
All the best
Dario
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