Given an input genetic map and a maximum error rate, greedily drops positions to produce a map with fewer entries. Following processing, the only remaining map positions are those that, if dropped, would produce an error greater than the threshold (assuming linear interpolation for finding genetic positions).
To run on chromosome 17 of the HapMap II genetic map (http map link), with 0.02 cM of error tolerated, run:
./min_map.py -error 0.02 -chr 17 -mapfile /path/to/genetic_map_GRCh37_chr17.txt
This produces min_viable_map17.txt with the subsetted genetic map. (Use
-out to change the output prefix; default is min_viable_map.)
Use ./min_map.py -h for a list of options. If using a genetic map that
doesn't match the format of the HapMap map, be sure to set -physcol for the
physical position column and -genetcol for the genetic position column.
By default, the script assumes the input map has a header, which it deletes.
Use -noheader to treat all the input lines (except those that begin with
#) as map entries.
To run on a sex-specific genetic map, combine the male and female maps into
separate columns in a single input file (for each chromosome). You can then
call ./min_map.py with -sexspecific and set -genetcol to the column with
one of the two genetic positions (male or female) and -genet2col to the
other.