Well there are a few reasons this could happen. selscan will filter low
frequency sites (default MAF 0.05), so it is possible that may sites are
being filtered. If the sites are sparsely distributed along the genome, it
is possible that large gaps are preventing computations (can be modified
with --max-gap). Did you get any warning messages in the log file?
Zachary
On Wed, May 11, 2022 at 10:10 AM meimingWu @.***> wrote:
Hi, I have a question, when I run the following command to calculate iHS,
there is run log output, but the result file is empty. I saw the following
description: "Selscan is 'dumb' with respect ancestral/derived coding and
simply learning haplotype data to be coded 0/1." There are lots of 0/0 in
my VCF file. Is this the reason why the output file is empty? Hope to get
your reply, thank you!
Hello,
Well there are a few reasons this could happen. selscan will filter low frequency sites (default MAF 0.05), so it is possible that may sites are being filtered. If the sites are sparsely distributed along the genome, it is possible that large gaps are preventing computations (can be modified with --max-gap). Did you get any warning messages in the log file?
Zachary
On Wed, May 11, 2022 at 10:10 AM meimingWu @.***> wrote: