Incorrect CIGAR string found. CIGAR string can only have I/D/H/S/X/=

schneebergerlab / fixchr

MIT License

13 stars 1 forks source link

Closed cfz1998 closed 1 year ago

cfz1998 commented 1 year ago

./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf 
fixchr -c aln.paf -r asm1.fa -q asm2.fa -F P

I got an error:

Hi! @mnshgl0110 . How to fix it?

Thank you for your reply!

mnshgl0110 commented 1 year ago

Sorry for the missing documentation. Please use the --eqx parameter of minimap2 as described here.