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Obtaining Quality score of the mapped sequences - BBMap

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

alignment
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updated by madzayasodara • madzayasodara • written by madhu.9124 • madhu.9124

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.

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written by GenoMax GenoMax

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

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written by madhu.9124 • madhu.9124

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

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written by GenoMax GenoMax

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

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written by madhu.9124 • madhu.9124

missing ' after

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

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written by Arup Ghosh Arup Ghosh

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

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written by GenoMax GenoMax

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...

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written by madzayasodara • madzayasodara

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]
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written by Istvan Albert Istvan Albert

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