Question

Any suitable alternative for Haploview?

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4.2 years ago

Mahan ▴ 70

Hello everyone, I used to use Haploview to analyze my GWAS results but recently I'm unable to use it because of some errors it throwing. I would like to know if there is any suitable alternative for Haploview which can help me to visualize my GWAS results and also look into SNPs by beta, OR, and p-value, etc.

Thanks in advance

Haploview Alternative GWAS Manhattan Plot • 2.2k views

ADD COMMENT • link 4.2 years ago by Mahan ▴ 70

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Hi Kevin, thanks for your tips. Can you please point me a suitable page for this "For the beta, OR, p-value, et cetera, please use PLINK."? Thanks in advance

ADD REPLY • link 4.2 years ago by Mahan ▴ 70

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Hi, please try the PLINK documentation. There is the original documentation for PLINK pre version 1.9 ( https://zzz.bwh.harvard.edu/plink/ ) and the 'new' documentation for versions >= 1.9 ( https://www.cog-genomics.org/plink/ ).

ADD REPLY • link 4.2 years ago by Kevin Blighe 88k

score 3 · Answer 1 · 2020-09-05

Yes and no... this is a 'forgotten' space, i.e., haplotype viewers. You may get some tips from this thread: A: Manhattan plots and linkage disequilibrium heatmap

For beta, OR, p-value, et cetera, please use PLINK. In R, try snpStats ( http://bioconductor.org/packages/release/bioc/html/snpStats.html )

Kevin