Hi, I have a SNP dataset containing 717045 SNPs. I want to a GWAS using Haplotype blocks. But I do not know first how to create haplotype SNP dataset for GWAS and also the criteria for creating haplotype blocks. My dataset is in VCF format.
Can someone please give me some ideas on how to make a haplotype dataset for GWAS? Also which software to create haplotype blocks?
Regards
Anik Dutta
Hi Anik
you'll need some bioinformatics stuffs as you'll see in this wiki page (https://en.wikipedia.org/wiki/Genome-wide_association_study). it's quite simple but you got some working days.
fred
Hi Anik,
You should be able to use Plink for this: https://www.cog-genomics.org/plink/1.9/ld
Another option would be to use Haploview (you can load plink files into this software) however I don't think you can load data from across chromosomes and there is likely an upper limit on the number of SNPs/length in Kb for the input data too. Perhaps this might be good to visualize some of the data only/check any loci of interest.
I hope that helps
Amy
Conceptually, haplotype-based analysis can be done with any user-defined haplotype including synthetic bins, LD blocks, specific combination of SNPs, etc. For example, you can simply test 20-SNPs at a time and call it a haplotype. If you decide to test a fixed number of SNPs at a time, notice that to avoid losing power you may want to treat these sets of SNPs as a single random effect or use the first principal component (Eigenvector) of the matrix containing the haplotype (Nx20).
Cheers
AX
Hi Sophie Limou thank you very much for the information. My SNP data file is already filtered. But it is not imputed and contains some missing data. Will it cause any problem in the haplotype building? Furthermore, I have some multi-allelic SNPs which I do not want to remove. Can ShapeIT handle multi-allelic SNPs? or do you know any other tools for building haplotype from data file containing some multi-allelic SNPs?
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