Question: Making Linkage Disequilibrium blocks from SNPs position for NCBI Build 38
0
gravatar for Bahar
21 months ago by
Bahar40
Iran
Bahar40 wrote:

Hello evryone

I'd like to know if anyone has or might know how can I make LD block from my SNPs list for the last human genome build (GRCh38). I'm currently working on the GWAS Iranian population. I'm trying remove high LD regions from my dataset in QC prosses.

I using of plink r2 command for finding connected SNPs. but I can't find the best way for estimating region LD blocks!

anyone can help me

Thanks a lot in advance for the attention!

population study ld qc gwas • 812 views
ADD COMMENTlink modified 21 months ago by chrchang5233.1k • written 21 months ago by Bahar40
1
gravatar for Denise - Open Targets
21 months ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.4k wrote:

Have you checked the LD data in Ensembl e.g. rs1333049. This is the plot for that variant and help on the Linkage disequilibrium data is also available.

ADD COMMENTlink written 21 months ago by Denise - Open Targets4.4k
1
gravatar for reza.jabal
21 months ago by
reza.jabal250
United Kingdom
reza.jabal250 wrote:

If you are carrying out a GWAS in Iranian population you have to select your tag SNPs from the same population, otherwise you introduce population stratification bias into your data! This means that you cannot select your tag SNPs from the reference population and then genotype your samples at those loci!

ADD COMMENTlink written 21 months ago by reza.jabal250
1
gravatar for chrchang523
21 months ago by
chrchang5233.1k
United States
chrchang5233.1k wrote:

The plink --blocks command is designed for this.

ADD COMMENTlink written 21 months ago by chrchang5233.1k
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