Forum:Plink calculator for calculating pairwise LD

Question

[mandecent.gupta]

Hi,

I have list of snps in vcf format. Can plink LD calculator be used for pairwise LD calculation?

Regards

[Giovanni M Dall'Olio]

Note that vcftools has options to calculate r2: http://vcftools.sourceforge.net/man_latest.html#OUTPUT

[zx8754]

Plink2 can read VCF files, did you try loading VCF then running --r2?

[mandecent.gupta]

Thanks for prompt reply. I am using followning command

./plink --vcf sample2.vcf

and getting following error.

where sampl2.vcf file is prepared from Example: http://www.1000genomes.org/node/101

PLINK v1.90b3g 64-bit (5 Mar 2015)         https://www.cog-genomics.org/plink2
(C) 2005-2015 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
516842 MB RAM detected; reserving 258421 MB for main workspace.
Error: Improperly formatted .vcf header line.

[zx8754]

From GitHub code, I think plink expects tab delimited.

if (memcmp(bufptr, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO", 38)) {
logprint("Error: Improperly formatted .vcf header line.\n");
...

Below works for me,

wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/exon/snps/CEU.exon.2010_03.genotypes.vcf.gz
/plink_1.9/plink --vcf CEU.exon.2010_03.genotypes.vcf.gz --r2 --out temp