gwaslab 3.3.2

A collection of handy tools for GWAS

gwaslab

Note: Some part of the docs are outdated. I am currently updating the documents.

• A simple python package for handling GWAS sumstats.
• Each process is modularized and can be customized to your needs.
• Most manipulations are designed as methods of python object, gwaslab.Sumstats.

Please check GWASLab document at https://cloufield.github.io/gwaslab/

import gwaslab as gl
# load plink2 output
mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
             fmt="plink2",
             build="19")

# or you can specify the columns:
mysumstats = gl.Sumstats("t2d_bbj.txt.gz",
             snpid="SNP",
             chrom="CHR",
             pos="POS",
             ea="ALT",
             nea="REF",
             neaf="Frq",
             beta="BETA",
             se="SE",
             p="P",
             direction="Dir",
             n="N",
             build="19")

# manhattan and qq plot
mysumstats.plot_mqq()
...

Functions

Standardization, Normalization & Harmonization

• CHR and POS notation standardization
• Variant POS and allele normalization
• Genome build : Liftover
• Reference allele alignment using a reference genome sequence
• rsID assignment based on CHR, POS, REF and ALT
• CHR POS assignment based on rsID using a reference VCF
• Palindromic SNPs and indels strand inference using a reference VCF
• Check allele frequency discrepancy using a reference VCF

Quality control, Value conversion & Filtering

• Statistics sanity check
• Equivalent statistics conversion
  • BETA/SE , OR/OR_95L/OR_95U
  • P, Z, CHISQ, MLOG10
• Extract/exclude hapmap3 variants
• Extract/exclude MHC variants
• Filtering values.

Visualization

• Mqq plot : Manhattan plot and QQ plot side by side (with a bunch of customizable features including auto-annotate nearest gene names)
• Heatmap : ldsc-rg genetic correlation matrix
• Scatter Plot : variant effect size comparison with sumstats
• Scatter Plot : allele frequency comparison
• Forest Plot : forest plots for meta-analysis of SNPs
• Examples

Other Utilities

• Read ldsc h2 or rg outputs directly as DataFrames (auto-parsing).
• Extract lead variants given a sliding window size.
• Extract novel loci given a list of known lead variants.
• Logging : keep a complete record of manipulations from raw data to munged data.
• Sumstats summary function: know your data better.
• Formating GWAS sumstats in certain formats
  • LDSC / MAGMA / METAL / MR-MEGA / FUMA / VCF / BED... check available formats

Install

pip install gwaslab==3.3.2

Requirements:

• Python >= 3.6
• pySAM
• pyensembl
• scikit-allel
• Biopython >= 1.79
• liftover >= 1.1.13
• pandas >= 1.2.4
• numpy >= 1.21.2
• matplotlib >=3.5
• seaborn >=0.11.1
• scipy >=1.6.2
• statsmodels > =0.13
• adjustText

Contacts

• Github: https://github.com/Cloufield/gwaslab
• Blog (in Chinese): https://gwaslab.com/
• Email: [e-mail]