Question: Meaning of Base Alignment Quality (BAQ) 0
4
gravatar for Andreas
4.9 years ago by
Andreas2.4k
Singapore
Andreas2.4k wrote:

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:

baq0 tview screenshot

 

Can anyone explain this?

 

Many thanks,

Andreas

ADD COMMENTlink modified 4.9 years ago by Jordan1.1k • written 4.9 years ago by Andreas2.4k

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

ADD REPLYlink written 4.9 years ago by Andreas2.4k
0
gravatar for Jordan
4.9 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

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.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Jordan1.1k

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

  

ADD REPLYlink written 4.9 years ago by Andreas2.4k
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