Entering edit mode
2.3 years ago
sshen2021
•
0
Hi all,
Was wondering if anyone knew whether there exists a VCF version of the Neale Lab 2018 GWAS variants? I can’t seem to find one on the website but I might be mistaken…
Alternatively, is it possible to convert the variant file (located here https://docs.google.com/spreadsheets/d/1kvPoupSzsSFBNSztMzl04xMoSC3Kcx3CrjVf4yBmESU/edit#gid=178908679) to VCF format? I have never done this before so I'm not sure where to start...
Thank you for your help!
A google query returns: http://www.nealelab.is/uk-biobank
How does this answer OP's question? I think this should be a comment, not an answer and I'm moving it to one now.
due to the links found in that site and the linked github repository, in my view, it constitutes an answer to the question.
Best, VAL
I disagree. It's a general pointer to a link that could answer OP's question, but it's not a definite answer. Such pointers belong in comments.
Why do you need it in VCF format? You can create a VCF out of the TSV but most VCF-specific information will need to be extrapolated/filled-in with fake values. Can your pipeline work with tabular data?
If you can't do without VCF, email the Neale Lab (as stated in the file you linked to): nealelab dot ukb at gmail dot com