Understanding SAM file format
Hello All,
I am trying to understand the sam output from the alignment. following is example:
[query_name] 16 [Chr_name] [position] 28 [cigar] * 0 0 [long_seq] * NM:i:11017 ms:i:912 AS:i:882 nn:i:0 ts:A:+ tp:A:P cm:i:170 s1:i:835 s2:i:0
from This link I understand the what the first 11 field means. However, I am unable to understand the fields after 11th fields. Can someone help me understand them?
Thank you in advance.
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Pierre Lindenbaum
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KVC_bioinfo
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KVC_bioinfo
1 answer
In the link you gave, look at section 1.5 "The alignment section: optional fields." It says
All optional fields follow the TAG:TYPE:VALUE format where TAG is a two-character string that matches /[A-Za-z][A-Za-z0-9]/
And it explains what those tags, types, and values are.
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Hussain Ather
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The fields after 11th field are optional fields. Hope this link helps. It listed all the optional fields specification.
https://samtools.github.io/hts-specs/SAMtags.pdf