thanks you, it works but after incrementing the values, I want to save the changes to the same same file.
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Increase the fifth column ( MAPQ) value in Sam file
Hi,
I have a sam file and I want to increase the value present in the fifth column of the sam file ( MAPQ). This is done to test the BBMap application. Kindly help.
Thanks
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1 answer
Hi madhu.9124,
Such tasks are typically done using awk or perl. Here's one solution:
cat alignment.sam | awk -v OFS='\t' '$5 += 7'
This will increase MAPQ (field 5) by 7.
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You can use awk -i inplace -v OFS='\t' '$5 += 7' alignment.sam, but it's good practice to keep your original files.
This is what I would do:
cat alignment.sam | awk -v OFS='\t' '$5 += 7' > alignment_mapqincreasedbyseven.sam
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Just a couple of things... You should print the sam header as it is, without incrementing the 5th column. I.e. with something like if($0 ~ "^@") {print $0} else {...}. Also you should check that incrementing the MAPQ doesn't make it out of bound, i.e. no more than 254 (255 meaning not available).
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Good points! andthisistextfulfillsthesmartcharacterrequirement
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thanks a lot, it works.
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