How to generate haplotypes with SNPs from WGS ?
1
0
Entering edit mode
3 months ago

Hi,

I have a .vcf file with 150 000 SNPs on the X chromosome and genotypes for 5 samples from WGS.

I tried using plink. I exported the data in plink format :

vcftools --gzvcf ../rawData/FXXX_chrX_PASS_variants_hg38.vcf.gz --plink --out plink_X

Then I manually modified the .ped file so it take into account my pedigree. 3 males, 2 females. 2 cases, 3 controls. And I run the r2 function of plink.

plink --bfile plink_X --ld-xchr 1 --r2 -ld-window-kb 1 --ld-window 1000 --ld-window-r2 0 --out plink_X

The results are R2=1 everywhere no matter the size of the window.

I also tried the blocks function.

plink --bfile plink_X --ld-xchr 1 --blocks -ld-window-kb 1 --ld-window 1000 --ld-window-r2 0 --out plink_X

But no haploblocks found.

What I want is to know is the shared regions of the X chromosome for the 2 case samples. Does anyone know what I am doing wrong ? Or what else I can try ?

SNP plink haplotype • 204 views
ADD COMMENT
1
Entering edit mode
3 months ago

You can't compute meaningful LD stats with only 5 samples. (You also shouldn't be using vcftools to "export to plink"; plink --vcf is far better at that operation.)

A standard approach for estimating human haplotypes is to use a public reference dataset, such as 1000 Genomes, as an additional input to a phasing program like Eagle or SHAPEIT4.

ADD COMMENT
0
Entering edit mode

Thank you for your help ! I'll try this !

ADD REPLY

Login before adding your answer.

Traffic: 2679 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6