GCTA-COJO command and parameters

Shicheng_Guo · 4 May 2022 03:30

Dear Team,

Can you share me the exact GCTA-COJO command and parameters so that I can compare my results with opentargets result. I am interested in some difference result with my data.

Thanks.

Shicheng

ochoa · 9 May 2022 09:28

I believe this is what you are after:

github.com

opentargets/genetics-finemapping/blob/ed7146900518562f4513b6e24749a9089412d039/finemapping/gcta.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Ed Mountjoy
#

import subprocess as sp
import os
import pandas as pd

def get_conditional_top_loci(
        sumstats,
        in_plink,
        temp_dir,
        maf=0.01,
        cojo_p=5e-8,
        cojo_window=500,
        cojo_collinear=0.9,
        logger=None,
        split_ld=False

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GCTA-COJO command and parameters

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