Re: [Vcftools-help] question about vcftools when calculating LDs

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

Hi,

More info on this case. I already tried to scan all possible pairs that
within 200kb and with R2>0.8.
For the SNP
I did find a reasonable number of LD SNPs, such as

1 1287055 1310291 1006 1 0.00886629 1
1 1287055 1310821 1006 1 0.00886629 1
1 1287055 1310824 1006 1 0.00886629 1
1 1287055 1340126 1006 1 0.00886629 1
1 1287055 1344727 1006 1 0.00886629 1
1 1287055 1344761 1006 1 0.00886629 1

But this is too slow and not quite necessary. Could you please suggest what
is the problem in my code?

Thanks.

Jing


ᐧ

On Fri, Mar 30, 2018 at 12:39 PM, Jing Zhang <jin...@gm...>
wrote:

> 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...
> ᐧ
>



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