ERROR: Variant physical position must be monotonically increasing
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?
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