gwaslab 0.0.4

A collection of handy tools for GWAS

gwaslab

A collection of handy python scripts for GWAS.

1. Manhattan plot
2. QQ plot
3. Calculate lamda GC
4. Select top SNPs based on a given window size.
5. Convert beta/se <-> OR/95%L_U/95%L_L
6. Select hapmap3 SNPs from sumstats
7. Convert Observed scale heritability to liability scale heritability

Requirements:

1. Python>3
2. scipy
3. numpy
4. pandas
5. matplotlib
6. seaborn

Install:

pip install gwaslab

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Usage:

import gwaslab as gl

gl.mplot(df,chr,pos,p,cut,cutfactor)

gl.qqplot()

gl.gc()

gl.getsig()