Convert paf to delta format.
This script relay on the cs tags in the paf to determine the postions of indels.
Hence, the mapping commond should contain --cs:
minimap2 --cs target.fa query.fa > query_vs_target.paf
Then run:
perl paf2delta.pl query_vs_target.paf > query_vs_target.delta
The delta file generated can be used for delta-filter:
delta-filter -r -q -l 5000 query_vs_target.delta > query_vs_target.rq.delta