output sis.tsv and interpretation

[laurabuggiotti]

Hi,

im using rfmix v2 for cattle population genomics, and really enjoy it!
I have SNPs from whole genome sequence from several populations and im playing around with the tool to infer introgression.
I have few questions on the output i get:

• what is in the sis.tsv file?
• n snps in both sis.tsv and map.tsv, how they are calculated?

Moreover I been using different -w and would like to know if there is a formula I can use to estimate the right one given my datasets.

Thanks for your time and support and hope to hear from you soon!
cheers,
Laura

[laurabuggiotti]

just a quick update...i found that the n_snp is the number of snps overlapping between query and reference...sorry!