Key-value pairs at the end of lines of gaf/paf files

Question

[guntul]

Hi everyone, I dont understand what the optional strings at the end lines of paf and gaf files really mean? This link and this link explains the mandatory columns but not explain exactly what they means. Can you explain or give sources explaining it?

Answer 1

[cmdcolin]

it is very similar to the SAM file format in that you can have "extra information" about the alignment in those key-value pairs. sometimes they are referred to as tags (e.g. in this document "SAM tags" https://samtools.github.io/hts-specs/SAMtags.pdf) the same type of info can be added to PAF.

here is an example of a PAF line

ctgA    45141   0       45141   +       ctgA    50001   0       50001   45141   50001   60      NM:i:4860       ms:i:90254      AS:i:85398      nn:i:0  tp:A:P  cm:i:8494       s1:i:44546      s2:i:0  de:f:0.0000  rl:i:0  cg:Z:28498M4860D16643M

the cg tag is a "CIGAR" string, and various others are just what minimap2 generates by default in the PAF output.