Question

What do the samtools column names mean

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3.5 years ago

Ishak • 0

Can anyone explain more what do these items mean?

MRNM is the mate reference name. MPOS is the mate position (1-based, leftmost). ISIZE is the inferred insert size.

Thanks in advance

NGS samtools • 1.0k views

ADD COMMENT • link updated 3.5 years ago by Ram 44k • written 3.5 years ago by Ishak • 0

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Please edit your post and make the title better. Your question has nothing to do with samtools - it is about tags in the SAM format. Have you tried reading the SAM/BAM specification? How far along did you get?

ADD REPLY • link 3.5 years ago by Ram 44k

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Thanks for your note. I am new here and definitely, I will take in account your comment.

I read that MRNM has = or * . What is the different between two symbol?
my file case has (-160) as ISIZE, what does symbol ( - ) mean?

The pdf file doesn't mention this point

Thank you

ADD REPLY • link updated 3.5 years ago by Ram 44k • written 3.5 years ago by Ishak • 0

score 1 · Answer 1 · 2021-06-02

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3.5 years ago

Istvan Albert 101k

As the commenters pointed out the answers to the question are in the Samtools specification:

https://samtools.github.io/hts-specs/SAMv1.pdf

It is not an easy read, that's for sure, but just keep at it.

ADD COMMENT • link 3.5 years ago by Istvan Albert 101k