Closed biozzq closed 3 years ago
Hi there,
So if you are running ihs
or nsl
scans, selscan
will only compute the statistics at sites with MAF >= 0.05 (change with --maf
) and by default sites with MAF < 0.05 are filtered (modify with --keep-low-freq
).
If you are running XP-EHH or XP-nSL scans, no filtering is done and selscan will use all the sites provided. In this case, I think filtering sites that are monomorphic in the combined data is a good idea (but keep sites that are poly in one and mono in the other).
Hope this helps!
Dear @szpiech
Thank you.
Best wishes
Hi @szpiech
I am wondering if it is necessary to filter out the non-polymorphsim variants (e.g., all individuals are
0|0
or1|1
|) when usingselscan
, because I do not know how the number of SNPs was calculated inselscan
. Why dose this always happen in my study? I usually do genotype phasing for all my samples jointly, however, I want to identify the selection sweeps in subsamples. Thus, when not filtering by allele frequency for these subsamples, the non-polymorphsim variants will be kept in the input VCF forselscan
.Best wishes, Zheng zhuqing