More lines than SNPs in OmegaPlus report file

[Zoe Meziere]

Hello,

I am new to using OmegaPlus, so I might be missing something obvious. But first of all, thanks for developing such user-friendly tools!

I am successfully ran OmegaPlus with a VCF as input file, but the output report file has a lot more rows than I have SNPs in my VCF file. I have 2,437,389 SNPs and get 21214318 lines in the report file. Also, the position numbers look odd because they are not round integers. For example, I have:

5057.6450 2.162787
5058.2520 2.162787
5058.8589 2.162787
5059.4658 2.162787

This is the command I use to run OmegaPlus:

./OmegaPlus -name input.vcf \
-grid 100 \
-minwin 500 \
-maxwin 10000 \
-seed 123 \
-impute N \
-impute GAP

Any help would be appreciated :)

Kind regards