Hi all,
I'm trying to calculate iHS with selscan
: the program seems to apparently run normal, but my output file is empty.
I've phased my data with SHAPEIT
and tried the following commands:
selscan --ihs --vcf input.phased.vcf --map input.phased.map --out output.phased
selscan --ihs --hap input.phased.haps --map input.phased.map --out output.phased
I've read in this post that running the program with a vcf
instead of an haplotypes file should give no trouble, however the output file is empty.
My .map
file looks like this:
22 ID1 0 17075353
22 ID2 0 17301492
22 ID3 0 17306184
22 ID4 0 17306270
22 ID5 0 17315503
And my .haps
file looks like this:
22 ID1 17339003 A G 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0...
22 ID2 17347294 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1...
Please, does anyone see something I'm missing? Thank you very much in advanced!
When I calculated xpehh using selscan, I also encountered the same problem. It seems to run normal ,but the output file is empty,only the header. Really confused...