A user reported an error in the heterozygous SNP filtering script.
Turns out, in cases where one of the alleles of a heterozygous position is equal to the reference, vcfsimplify.py would not pick up on that and would export it as a homozygous SNP
example:
REF ALT INFO
A C,G 1/2 -> OK
A T 0/1 -> NOT OK
The second case has been fixed,
For the 84 tomatoes it reduces the data in approximately 15%.
No large differences have been found pre- and pos- bugfix.