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selscan not outputting ihs
1
Entering edit mode
18 months ago

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 vcfinstead of an haplotypes file should give no trouble, however the output file is empty. My .mapfile 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 .hapsfile 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!

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0
Entering edit mode
14 months ago

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...

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