In the package Stacks, the -m parameter specifies the read depth, i.e. the minimal number of reads required to identify and accept a locus. I'm using the denovo_map.pl script and subsequently the populations script to output an input file for Structure.

With respect to denovo, the manual (p. 26) says:

m — specify a minimum number of identical, raw reads required to create a stack.

Now, in the 'populations' script, the manual (p.24) says

m — specify a minimum stack depth required for individuals at a locus.

Now I wonder, if -m in 'denovo' sets the min nr of read per allele, and -m in 'populations' sets it per individual, should not this parameter in populations have at leats 2x its value in denovo? Otherwise, the filtering would favour homozygotes over heterozygotes.

Is my reasoning correct?