run snp2hla tool in windows subsytem for linux

Question

[anasjamshed]

I had 25 bcf files that I converted into vcf to read and also merged them in one file. Now I want to apply snp2hla to find markers A,b,c. How can I do in by using wsl? do I need to use wsl?

Answer 1

[Istvan Albert]

the tool you ask about seems to be a shell script that runs additional software like plink and beagle

both of these tools can be easily installed in a linux-like system using a tool like conda or micromamba

now snp2hla program seems fairly old, from 2016, so there may be changes to how the required software operates.

I would look at what the snp2hla program does, notably the file:

SNP2HLA/SNP2HLA.csh 

then running those steps separately and figuring out what takes place.

• Plink: https://zzz.bwh.harvard.edu/plink/
• Beagle: http://faculty.washington.edu/browning/beagle/beagle.html

[anasjamshed]

I feel we have to install java to run snp2hla