Meaning of Base Alignment Quality (BAQ) 0

Question

[Andreas]

Hi all,

Every now and then I see BAQ values of 0 in samtools' mpileups. I thought I understood the overall concept (http://www.ncbi.nlm.nih.gov/pubmed/21320865), 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 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:

Can anyone explain this?

Many thanks,

Andreas

[Andreas]

Cross-posted on samtools-help on 2014-10-13

Answer 1

[Jordan]

The BAQ scores are also dependent on the neighboring bases of the read. It might be that the absence of an indel before or after is causing BAQ at this position to be zero.

Did you do indel based realignment on these reads? It can be done using GATK. If not, I suggest doing Indel based realignment and then do recalibration of bases again. This should remove most errors.

[Andreas]

Hi Jordan,

The data was indel realigned and then quality recalibrated. But anyway, as you can see there are no indels at all. Even a wider or deeper view of that area doesn't show any indels. I'm not sure sure what you mean by absence of an indel.

Andreas