meaning of new symbols in samtools mpileup format?
1
0
Entering edit mode
10.2 years ago
Dejian ★ 1.3k

Samtools v1 is released. I found some new symbols in the samtools mpileup results. The command I used is samtools mpileup -l $snpPos -f $REFfa -sO -o res.mpileup samp.bam. In the 5th column of the result file, some new symbols appeared (see symbols = and ~ below). These are two examples of part of the long string:

.....T...........^$.^$.^$.^".^$.^".^$.^".
T.TTTT....TT...TT,,......,^~.^~.^~.^~.^~.

For most symbols, they are explained before. But what are the meaning of the new symbols colored in yellow? Is there a document mentioning these changes? Thanks!

samtools HTSlib snp pileup • 4.8k views
ADD COMMENT
0
Entering edit mode

If it's possible that you have MAPQs of 93 (~ minus 33) then these would be reasonable. Otherwise, something does seem off.

ADD REPLY
1
Entering edit mode

Sorry, Devon, I still don't quite understand what you mean. The 5th column of pileup output is read bases and the 6th column is base qualities. It seems that it is not related to MAPQ. Did you take it for a question about sam format (5th column is MAPQ)?

ADD REPLY
2
Entering edit mode
10.2 years ago

N.B., I moved this comment to an answer so others don't click through thinking this issue still needs addressing.

No, I didn't take it for a question about SAM files. The 5th column of the pileup format always also included MAPQ scores when an alignment starts (denoted by ^ followed by MAPQ+33). This is also mentioned in the link in your post (note the penultimate paragraph). Having said that, a MAPQ of '=' makes a bit more sense than '~', but perhaps your aligner outputs MAPQs that high.

ADD COMMENT
0
Entering edit mode

You are right. Thanks a lot.

ADD REPLY

Login before adding your answer.

Traffic: 2499 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6