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meta.json
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meta.json
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{
"meta_analysis.run_meta.do10k": true,
"meta_analysis.conf_template": "gs://covid19-hg-analysis/20211031/conf/2/json/{PHENO}.json",
"meta_analysis.phenos": "gs://covid19-hg-analysis/20211031/conf/main_phenos",
"meta_analysis.summary_files": "gs://covid19-hg-analysis/20211031/conf/2/main_phenos_files",
"meta_analysis.run_meta.add_rsids_af.docker": "gcr.io/covid-19-hg/meta:fe3de",
"meta_analysis.run_meta.add_rsids_af.file_ref": "gs://covid19-hg-analysis/dbsnp/dbsnp_hg38p13_b153_numerical.vcf.gz",
"meta_analysis.run_meta.add_rsids_af.p_thresh": 1e-5,
"meta_analysis.run_meta.filter_cols.docker": "gcr.io/covid-19-hg/saige:0.36.3.2-2",
"meta_analysis.run_meta.filter_cols.out_template": "COVID19_HGI_{PHENO}_20220403.txt.gz",
"meta_analysis.run_meta.filter_cols.p_thresh": 1e-5,
"meta_analysis.run_meta.filter_variants.docker": "gcr.io/covid-19-hg/plots:0.5",
"meta_analysis.run_meta.filter_variants.variant_shortlist": "gs://covid19-hg-analysis/20211031/SNPs.10k",
"meta_analysis.run_meta.gather.docker": "gcr.io/covid-19-hg/plots:0.5",
"meta_analysis.run_meta.gather.loglog_ylim": 200,
"meta_analysis.run_meta.gather.min_eff_prop": "1/3",
"meta_analysis.run_meta.method": "inv_var",
"meta_analysis.run_meta.opts": "--is_het_test --dont_allow_space",
"meta_analysis.run_meta.run_range.docker": "gcr.io/covid-19-hg/meta:fe3de",
"meta_analysis.run_meta.leave_most_significant_out.docker": "gcr.io/covid-19-hg/bioinformatics:0.7",
"meta_analysis.run_meta.leave_most_significant_out.meta_threshold": 5e-8,
"meta_analysis.run_meta.gather_lmso.docker": "gcr.io/covid-19-hg/bioinformatics:0.7",
"meta_analysis.run_meta.gather_lmso.min_eff_prop": "1/3",
"meta_analysis.run_meta.sumstat_to_vcf.docker": "gcr.io/covid-19-hg/bioinformatics:0.7",
"meta_analysis.run_meta.lift.b37_assembly_fasta": "gs://covid19-hg-analysis/resources/Homo_sapiens_assembly19.edit.fasta",
"meta_analysis.run_meta.lift.b37_assembly_dict": "gs://covid19-hg-analysis/resources/Homo_sapiens_assembly19.edit.dict",
"meta_analysis.run_meta.lift.chainfile": "gs://covid19-hg-analysis/resources/hg38ToHg19.over.chain.edit.gz",
"meta_analysis.run_meta.lift.docker": "gcr.io/covid-19-hg/picard:2.25.6.tabix",
"meta_analysis.run_meta.lift_postprocess.docker": "gcr.io/covid-19-hg/bioinformatics:0.7",
"meta_analysis.run_meta.sumstat_to_vcf_10k.docker": "gcr.io/covid-19-hg/bioinformatics:0.7",
"meta_analysis.run_meta.lift_10k.b37_assembly_fasta": "gs://covid19-hg-analysis/resources/Homo_sapiens_assembly19.edit.fasta",
"meta_analysis.run_meta.lift_10k.b37_assembly_dict": "gs://covid19-hg-analysis/resources/Homo_sapiens_assembly19.edit.dict",
"meta_analysis.run_meta.lift_10k.chainfile": "gs://covid19-hg-analysis/resources/hg38ToHg19.over.chain.edit.gz",
"meta_analysis.run_meta.lift_10k.docker": "gcr.io/covid-19-hg/picard:2.25.6.tabix",
"meta_analysis.run_meta.lift_postprocess_10k.docker": "gcr.io/covid-19-hg/bioinformatics:0.7"
}