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What do the samtools column names mean

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
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updated by Ram Ram • written by Ishak • Ishak

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?

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written by Ram Ram

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

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updated by Ram Ram • written by Ishak • Ishak

1 answer

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.

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written by Istvan Albert Istvan Albert

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