Obtaining Quality score of the mapped sequences - BBMap

Question

[madhu.9124]

Hi,

I am new to BBMap, so I kindly request to help me to find the **quality score of the mapped sequences. I also want to increase the quality score of the mapped sequence.

Thanks Madhu

[GenoMax]

Are you referring to alignment scores (MAPQ values, column 5)? Those are in the SAM/BAM files. Otherwise this question is missing what it is you are looking for.

[madhu.9124]

thanks, I want the MAPQ value. Any idea of the command to get the MAPQ value using SAMtool.

[GenoMax]

What will you do with standalone MAPQ values? You could do something like samtools view test.bam | awk -F "\t" '{print $5}' OR awk -F "\t" '{print $5}' your_file.sam

[madhu.9124]

thanks a lot, I just want to retrieve the value and increase the value to test the BBMap application.

[Arup Ghosh]

missing ' after

awk -F "\t" '{print $5}

[GenoMax]

Added to post above and here awk -F "\t" '{print $5}' your_file.sam

[madzayasodara]

You guys sure there's not a sam/bamtools cmd that straight up does this? I did my alignment using BWA. I could loop through my 23 whole-genome bam files doing this, but It's gonna be real slow...

[Istvan Albert]

the original question is somewhat undefined. What is the purpose of extracting the mapping quality?

If one wanted to filter alignment by a minimal score this can be done with

samtools view -q 10 myfile.bam

where

 -q INT   only include reads with mapping quality >= INT [0]