├── .gitignore ├── LICENSE ├── Liftover_SNP.py ├── PLINK_file_Utils.py ├── README.md ├── __init__.py ├── annotation.py ├── aud_meta_qq_lambdas.ipynb ├── config.plotgwas.3.cfg ├── convert_cleansumstats_output_to_mixer_format.py ├── data └── biomart_GENCODE_basic.txt.gz ├── fdrmat2csv.py ├── figs └── Z3nns.png ├── lift_rs_numbers.py ├── make_ld_matrix ├── README.md ├── data │ └── EUR_subj.list ├── genotypes2ref.py ├── make_ld_matrix.py └── make_maf_vector.py ├── make_universal_variant_ids.py ├── manhattan.py ├── merge_bed_files.py ├── overCorrect.py ├── plink_utils.py ├── plotgwas.py ├── process_metal.py ├── pyliftover ├── GRCh37ToHg19.over.chain.gz ├── README ├── __init__.py ├── chainfile.py ├── hg17ToHg19.over.chain.gz ├── hg18ToHg19.over.chain.gz ├── hg19ToGRCh37.over.chain.gz ├── intervaltree.py └── liftover.py ├── qq.py ├── sumStats2ref.py ├── summary_stats_Utils.py ├── sumstats.py ├── sumstats2mat.py ├── sumstats_ldsc_helper.py ├── sumstats_utils.py ├── tests ├── 1234_ref.bim ├── case01.mat ├── case01.txt ├── case01.txt.gz ├── case02.txt ├── case02.txt.gz ├── case03.txt ├── case03.txt.gz ├── case04.mat ├── case04.txt ├── case04.txt.gz ├── test_consistent.py └── test_duplicated.py └── version.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/precimed/python_convert/HEAD/LICENSE -------------------------------------------------------------------------------- /Liftover_SNP.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/precimed/python_convert/HEAD/Liftover_SNP.py -------------------------------------------------------------------------------- /PLINK_file_Utils.py: 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