ERROR: Variant physical position must be monotonically increasing

Question

[reza]

I want to calculate XPEHH for each SNP position. When I run the following command

selscan --xpehh --vcf B10_beagle.vcf --vcf-ref D6_beagle.vcf --map MAP.map --threads 8 --out B10vsD6

I get this error

ERROR: Variant physical position must be monotonically increasing
Ch2:66 66 appears after Ch1:124715015 1247150

my solution for this problem is sorting map file based on SNP position by

sort -nk 4 MAP.map > MAP_sorted.map

running selscan with MAP_sorted.map solved this error, now my question is, my way to solve this error is correct?

[LauferVA]

Should be ok, can verify by writing a quick script to check chromosome & position from vcf and check against the map, then added confirmation by actually confirming using bash or python