Good afternoon everyone, I'm new to bioinformatics, I wanted to see if you could help me. I need to do a linkage disequilibrium analysis of some Saccharomyces cerevisae samples I have, I got the data and files (.vcf) using NGSEP (used for QTL mapping) when I was doing other research. Now I need to do this quantification of the LD from this .VCF file containing 4 samples, two haploid, two diploid. I thought about using Plink because I found it in the bibliography, do you guys recommend something to start with plink? tips on the parameters or anything useful that would be nice for me to know? I would also like to know if you know how I can get the Saccharomyces cerevisae SnpId ? as I thought of using the LDSC program. Thank you for your attention.
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written
by
DOUGLAS •
1 answer
Unfortunately, 4 samples is far too few for LD analysis. (plink2 now prints an error message if you attempt LD analysis with fewer than 50 samples.)
Yes, I'm serious, for the statistical analyses that plink supports.
I have deleted the other misleading answer.
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