munge_sumstats_beforeQC.json

{
    "munge_sumstats.sumstats_loc": "gs://gbmi-analysis/08202020/conf/upload_loc_pop_09062020.txt_refined_Estonian",
    "munge_sumstats.gnomad_ref_template": "gs://gbmi-analysis/gnomad/v3/filter/gnomad_v3_b38_ref_POP.gz",
    "munge_sumstats.clean_filter.docker": "gcr.io/global-biobank-meta-analysis/saige:0.39.3",
    "munge_sumstats.clean_filter.af_col": "AF_Allele2",
    "munge_sumstats.clean_filter.min_mac": 20,
    "munge_sumstats.clean_filter.N_col": "N", 
    "munge_sumstats.clean_filter.Ncontrol_col": "N.Controls", 
    "munge_sumstats.clean_filter.Ncase_col": "N.Cases", 
    "munge_sumstats.clean_filter.min_info": 0.3,
    "munge_sumstats.lift.docker": "gcr.io/global-biobank-meta-analysis/meta:4bd49",
    "munge_sumstats.lift.b37_ref": "gs://gbmi-analysis/recomb_map/37/plink.chr21.GRCh37.map.txt",
    "munge_sumstats.lift.b38_ref": "gs://gbmi-analysis/recomb_map/38/plink.chr21.GRCh38.map.txt",
    "munge_sumstats.harmonize.options": "",
    "munge_sumstats.harmonize.docker": "gcr.io/global-biobank-meta-analysis/meta:4bd49",
    "munge_sumstats.plot.docker": "gcr.io/global-biobank-meta-analysis/plotv2:0.3", 
}