For example, the first alignment in my SAM file currently looks like
08b20551-b31c-4170-a04c-40a34ee8b71f 0 chr20 4699371 60 272H123M637H * 0 0 CCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAA &'$'()+2220/,+.203:=?65<?BDDCF:B@>69;AF?FLA=?CB>=83/0-@@?=>@A52.;AA@CGA45=DFHG@?A?;<9A:A>=:=8<=@=B56B:@@BCHFHG?4@<::=98=:79 ms:i:1920 AS:i:1920 nn:i:0 tp:A:P cm:i:158 s1:i:929 s2:i:0 de:f:0.0148 rl:i:0 HP:i:2 PC:i:30 PS:i:4688888
I would like to delete the MAPQ (aka qual) component. Expected:
08b20551-b31c-4170-a04c-40a34ee8b71f 0 chr20 4699371 60 272H123M637H * 0 0 CCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAA ms:i:1920 AS:i:1920 nn:i:0 tp:A:P cm:i:158 s1:i:929 s2:i:0 de:f:0.0148 rl:i:0 HP:i:2 PC:i:30 PS:i:4688888
How may I do this?
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written
by
francois •
Looks like you don't want to replace the mapping quality (MAPQ), but the base call quality (QUAL) instead. Mapping quality is 60 in your example.
Ah you're right, my bad!
I found a suitable solution:
cat in.sam | awk -v OFS='\t' '$11="*"' > out.sam
Not particularly elegant because it affects the header lines as well, but good enough for what I am currently doing...
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You will break SAM format if you do that. Why not ignore it if you are not interested in it? Or did you mean to replace the current value?
Ah, I see. A batch of my samples has
*for the MAPQ field, but this file has the full MAPQ info. I need to have the formats to match for downstream analysis.So yes, replacing with
*would work. Even better, actually.How can I do that?
You have
60in your example above for MAPQ field number 5.*is forRNEXTfield.See SAM format spec.