Why sam and paf have different number of lines?

Question

[PeterWu]

I've tried to run minimap2 using same parameters, one output in SAM format and one PAF format. Are these two files supposed to have same number of lines(except the header in SAM file)? I've observed that SAM file has less lines. Thanks a lot.

[Nicolas Rosewick]

Could you put the minimap2 command you used ?

[PeterWu]

I sort of know how thing's works, if there's skipped region from the reference(N is cigar) paf will have multi records

Answer 1

[WouterDeCoster]

I think you can find the solution in these issues:

• https://github.com/lh3/minimap2/issues/158
• https://github.com/lh3/minimap2/issues/218