Hi all,
every now and then I see BAQ values of 0 in samtools' mpileups. I
thought I understood the overall concept, but now I'm not sure
anymore. Does a value of 0 indicate this base is misaligned for sure?
How can that ever be the case? Also, I see this happening in nicely
aligned regions (all MQ60; not a lot of SNVs) with no indels anywhere
nearby. It's seems to be mainly happening close to the end of reads
and I see the same behaviour in samtools 0.1.19 and 1.0.
Here's an example: how can the second C every get a BAQ of 0?
Pileup information first (with base qualities translated into phred
scores), followed by a screenshot of tview:
# BAQ off
samtools mpileup -B -Q 0 $BAM -f $REF -r chrX:46918110-46918110
chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 30 34
36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36
# BAQ on
samtools mpileup -Q 0 $BAM -f $REF -r chrX:46918110-46918110
chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0
36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36
# extended BAQ
samtools mpileup -E -Q 0 $BAM -f $REF -r chrX:46918110-46918110
chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0
36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36
Screenshot of tview of the same region:
https://dl.dropboxusercontent.com/u/4119940/baq0.png
Can anyone explain this?
Many thanks,
Andreas
PS: This was cross-posted on https://www.biostars.org/p/115071/#115112
--
Andreas Wilm
andreas.w...@gmail.com | m...@andreas-wilm.com | 0x7C68FBCC
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