[Vcftools-help] question about vcftools when calculating LDs

[Jing Z. <jin...@gm...>]

Hi,

I was trying to extract SNPs with LD>0.8 for a list of input SNPs based on
EUR population from 1kg phase vcf files. I have tried several ways met
several problems. Would you please help. Thank you very much.

1. I extracted EUR samples and used the following command
"*vcftools --vcf f.vcf --ld-window-bp 200000 --hap-r2-positions
positions.list  --min-r2 0.8 --out prefix*"
the positions list file is like:
1       1287055
1       7917076
1       8095500
However, most of SNPs have no LD SNPs found. I did chrom by chrom, for
those returned, they only return no more than LD SNPs for only 1
orginal SNPs . While I used other web-based tools and returns quite a lot
of LD SNPs.

2. Then I also tried to use PLINK. However, the 1kg phase3 data
have multiallelic positions, which have >1 lines in the vcf files. I also
tried "--min-alleles 2 --max-alleles 2 " to remove but it does not work.
Then PLINK will always give me an error because of this duplicates.

Would you please suggest in this case?

Thank you very much!


-- 
Jing Zhang
---------------------------------------------------------------
Associate Research Scientist,
Molecular Biophysics & Biochemistry,
Computational Biology and Bioinformatics,
Yale University
___________________________________
Email: jin...@gm..., j....@ya...
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