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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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Regional plots with LD #83

Open xEmz opened 8 months ago

xEmz commented 8 months ago

Hi Yunye,

I want to make regional plots with LD (using the hg19 vcf) in GWASLAB. However, this seems to take forever to run. Do you know how this can be sped up?

Kind regards, Emma

Cloufield commented 8 months ago

Hi Emma, I am wondering if tabix is avaialble in your environment path? GWASLab will use tabix if available in environment path. If not, it will just iterate through the entire VCF file, which might be extremely slow if the VCF is large.