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Old 04-21-2011, 01:17 AM   #1
dariober
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311
Default How does "mpileup -Q" option work?

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:
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
I'm using samtools 0.1.15. Am I missing something obvious here?

All the best

Dario
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Old 01-31-2012, 01:24 PM   #2
ramensky
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Location: Los Angeles, CA

Join Date: May 2010
Posts: 1
Default

Hi, I had the same confusion, too. My experience is that -Q affects the output only in the BCF output mode (invoked with -u or -g), but not in the pileup mode, as in your example. In the meantime, -q (min read mapping quality) applies to both output modes.

Hope this helps.

Last edited by ramensky; 02-02-2012 at 03:43 PM.
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