The work has been moved to: https://github.com/atgu/GWASpy
A Python package for performing GWAS QC.
For now you can install preimp_qc using the command below. In the near future, it will be uploaded to pypi
pip install -r requirements.txt
python setup.py sdist
pip install dist/preimp_qc-0.1.0.tar.gz$ preimp_qc --dirname TestData/ --basename Basename --inputType plink --reference GRCh37
in the example above, inside the directory TestData, there must be three PLINK file Basename.*{bed,bim,fam}| Argument/ Option | Description |
|---|---|
--dirname |
Path to where the data is |
--basename |
Data basename |
--inputType |
Input type, plink or vcf |
--annotations |
Annotations file to be used for annotating the VCF file (ONLY for VCF input) |
--reference |
Reference genome build e.g. GRCh37, GRCh38 |
--qc_round |
The number of times QC has been performed on the data. Use 1 if it's the first round |
--pre_geno |
include only SNPs with missing-rate < NUM (before ID filter), important for post merge of multiple platforms |
--mind |
include only IDs with missing-rate < NUM |
--fhet_y |
include only female IDs with fhet < NUM |
--fhet_x |
include only male IDs with fhet > NUM |
--geno |
include only SNPs with missing-rate < NUM |
--midi |
include only SNPs with missing-rate -difference ("case/control) < NUM |
--withpna |
include monomorphic (invariant) SNPs |
--maf |
include only SNPs with MAF >= NUM |
--hwe_th_con |
HWE_controls < NUM |
--hwe_th_cas |
HWE_cases < NUM |