Question: Bwa-Mem - Where Has Sm:I Gone?
0
gravatar for steve
4.3 years ago by
steve40
steve40 wrote:

This question is a follow up from: Are some sequences uniquely mapped by BWA when mapped as paired-end that would not be when mapped as single-end?

My question is:

How does BWA-MEM report single-end mapping quality?

BWA-backtrack kindly reports the single-end mapping quality using the SM:i tag. But is there a way (hackish or otherwise) to get BWA-MEM to report this field? If not, why?


EDIT:

These tags would also be nice:

XT; XA; X0;

samtools bwa • 1.8k views
ADD COMMENTlink modified 4.3 years ago by Istvan Albert ♦♦ 74k • written 4.3 years ago by steve40
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gravatar for Istvan Albert
4.3 years ago by
Istvan Albert ♦♦ 74k
University Park, USA
Istvan Albert ♦♦ 74k wrote:

The mapping quality is reported in the 5th column of the SAM file (MAPQ).

ADD COMMENTlink written 4.3 years ago by Istvan Albert ♦♦ 74k

So for BWA-MEM, is SM:i always equal to MAPQ? Is that why Heng removed this from the output? IF that's the case I can just duplicate the field. easy.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by steve40

these are slightly different meanings of mapping qualities some discussion is here

Differing BWA MAPQ scores for a read depending on how I build the transcriptome

the way mapping qualities are obtained are somewhat mysterious and perhaps it is better there is only one of them

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Istvan Albert ♦♦ 74k

Any thoughts on how MAPQ is assigned?

ADD REPLYlink written 2.9 years ago by amirmhzadeh70
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