Question: How to do a Haplotype based GWAS?
0
gravatar for anikcropscience
8 months ago by
anikcropscience30 wrote:

Hello, this is my first post in this renowned group. Acutally, I am struggling with Haplotype based GWAS. I am doing GWAS on a plant pathogen. The single SNP GWAS has yielded any significant result. So, I have decided to use Haplotype based GWAS. I have a VCF file containing 717045 SNPs. I used Plink to generate haplotype blocks. It has yielded more than 74000 haplotype blocks. But I do not know how to use that data in the GWAS. From the plink output, the data is in .blocks or .blocks.det format.

Can someone please give me some ideas about how to use that data for GWAS? or How can I perform a Haplotype Based GWAS? Using which tool?

Looking forward to your reply. Thank you very much.

Regards Anik Dutta

snp plink genome • 475 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by anikcropscience30

Thank you very much Kevin. But the problem is, Ihave quite a few SNPs that are multiallelic and I do not want to loose them. So If I import those in Plink they are lost because plink only accepts biallelic SNPs. Do you have any suggestions on how can I keep those SNPs that are multiallelic?

Anik

ADD REPLYlink written 8 months ago by anikcropscience30

What if you split the multi-allelic records into individual records? This can be done with bcftools norm -m-any

ADD REPLYlink written 8 months ago by Kevin Blighe53k

This can be done with Vcftools or bcftools? Is bcftools included in Plink? Sorry, if the question is naive. I am new in this field.

ADD REPLYlink written 8 months ago by anikcropscience30

No, you would have to split these multi-allelic calls outside of PLINK, and then input the VCF file(s) back into PLINK.

ADD REPLYlink written 8 months ago by Kevin Blighe53k
1

Ok thanks a lot for the information.

ADD REPLYlink written 8 months ago by anikcropscience30
0
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe53k
Kevin Blighe53k wrote:

Hey, you are very welcome here.

If you use the older versions of PLINK (pre v1.9), you can simply use the --hap-assoc command line parameter. Take a look here: Multimarker haplotype tests

The feature does not seem to be implemented in version >=1.9. See the bottom of THIS page:

The .blocks file is valid input for PLINK 1.07's --hap command. However, the --hap... family of flags has not been reimplemented in PLINK 1.9 due to poor phasing accuracy (and, consequently, inferior haplotype likelihood/frequency estimates) relative to other software; for now, we recommend using BEAGLE 3.3.2 instead of PLINK for case/control haplotype association analysis. (You can use "--recode beagle" to export data.) We apologize for the inconvenience, and plan to develop variants of the --hap... flags which handle pre-phased data effectively.

You also have the option of exporting your data and creating your own statistical test, e.g., in R.

Kevin

ADD COMMENTlink written 8 months ago by Kevin Blighe53k
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