sorting of loci file for dense-snps

[nurmians]

sort -k1,1 -n 2,2n loci_unsrt.tsv > losi_sorted.tsv does not work.
Did you mean:
sort -k1,1n -k 2,2n loci_unsrt.tsv > losi_sorted.tsv
or
sort -k1,1 -k2,2n loci_unsrt.tsv > losi_sorted.tsv

Either way, it would be better just to say if you want the chromosomes in alphabetical or numerical (natural) order.

[nurmians]

Looks like the output of alleleCounter is identical for both inputs (alphabetical and numerically sorted).