Question: Making Linkage Disequilibrium blocks from SNPs position for NCBI Build 38
0
gravatar for Bahar
3.4 years 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 • 1.7k views
ADD COMMENTlink modified 3.4 years ago by chrchang5236.2k • written 3.4 years ago by Bahar40
1
gravatar for Denise - Open Targets
3.4 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k 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 3.4 years ago by Denise - Open Targets5.0k
1
gravatar for reza.jabal
3.4 years ago by
reza.jabal350
New York, USA
reza.jabal350 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 3.4 years ago by reza.jabal350
1
gravatar for chrchang523
3.4 years ago by
chrchang5236.2k
United States
chrchang5236.2k wrote:

The plink --blocks command is designed for this.

ADD COMMENTlink written 3.4 years ago by chrchang5236.2k
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