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BGI-shenzhen / PopLDdecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
MIT License
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EHH instructions not clear #4

Closed sergiopalmavera closed 3 years ago

sergiopalmavera commented 5 years ago

Hello!

trying to execute the EHH functionality built in PopLDdecay, I tried the following:

PopLDdecay -EHH 1:2750001 -InVCF vcf

And got this message: lack argument for the must

But it is not very clear what the message means.

Also, can a text file be used to provide the sites?

hewm2008 commented 5 years ago

Hi. With VCF files, PopLDdecay can also be used to calculate extended haplotype homozygosity (EHH) (Sabeti, et al., 2002) with the option of “-EHH” Output parameters are required，you must set the para [-OutStat],so you can try： 

./PopLDdecay -EHH 1:2750001 -InVCF  In.vcf   -OutStat  OutPrefix