Unmodifiable Conditional Analysis pipeline

Summary

Unmodifiable pipelines are predefined workflows that cannot be modified by the user. The advantage of running unmodifiable pipelines compared to modifiable pipelines is that you will get results directly to the green library and the User results PheWeb browser. No download requests are needed, because results of unmodifiable pipeline have been verified not to contain any individual-level data. Running the finemapping unmodifiable pipeline is very similar to running finemapping in the modifiable pipelines, with some small restrictions. The unmodifiable finemapping pipeline can be accessed in the sandbox from The pipelines app -> unmodifable workflow -> Unmodifiable Conditional DF12/13F13). For more information about the Pipelines tool, check the Pipelines tool documentation.

How it Works

The pipeline first take the input sumstats and runs the finemap pipeline to extract regions of interest. Then a step filters out regions where hits > locus_mlogp_threshold .

Then, regenie is called for each of these regions and rounds of conditional analysis are run until either the top hit is below the conditioning_mlogp_threshold or max_steps of iterations are reached.

Summary of inputs

  • regenie_cond_sb.sumstats_root: path to the sumstats. PHENO will be replaced by the pheno parameter.

  • regenie_cond_sb.prefix: the prefix of the output

  • regenie_cond_sb.pheno: Phenotype name. It needs to match the sumstats_root basename

  • regenie_cond_sb.regenie_conditional.null: Path to Loco of regenie step1.

  • regenie_cond_sb.pheno_file: Path to pheno file.

  • regenie_cond_sb.cov_file: Path to cov file.

  • regenie_cond_sb.is_binary: "true" or "false". it tells regenie whether the pheno is binary or not

  • regenie_cond_sb.covariates: List of covariates. The pipeline will filter them out to make sure only covaraites with >5 samples are included

  • regenie_cond_sb.chroms: Comma separated list of chroms to include.

  • regenie_cond_sb.regenie_conditional.max_steps: Maximum number of iterations in the conditional analysis

  • regenie_cond_sb.locus_mlogp_threshold: Mlogp threshold for the initial hit

  • regenie_cond_sb.conditioning_mlogp_threshold: Mlogp threshold for the conditioned hit

  • These are options for the finemapping threshold. They can be changed for users are familiar with the pipeline, but we recommend not touching them

    • regenie_cond_sb.finemap_regions.rsid_col: ""

    • regenie_cond_sb.finemap_regions.x_chromosome: "true"

    • regenie_cond_sb.finemap_regions.window: "1500000"

    • regenie_cond_sb.finemap_regions.scale_se_by_pval: "false"

    • regenie_cond_sb.finemap_regions.p_threshold: "0.00000005"

    • regenie_cond_sb.finemap_regions.max_region_width: "10000000"

    • regenie_cond_sb.finemap_regions.window_shrink_ratio: "0.9"

Outputs

There are two output files.

  • all_hits . A file that merges all pheno chains. This file contains all the steps done for each chain. In this case the first hits did not cause a chain as the new top hits in turn did not have significat pvalues. E.g.

    VARIANT
    BETA
    SE
    MLOG10P
    BETA_cond
    SE_cond
    MLOG10P_cond
    VARIANT_cond

    chr1_17381854_G_A

    -0.0371

    0.0064

    8.2425

    nan

    nan

    nan

    nan

    chr2_161145756_T_A

    -0.0429

    0.0073

    8.3533

    nan

    nan

    nan

    nan

    chr2_196338002_G_A

    0.059

    0.0095

    9.2624

    nan

    nan

    nan

    nan

    chr3_18633152_A_C

    0.044

    0.0067

    10.3279

    nan

    nan

    nan

    nan

    chr3_16811234_G_A

    -0.0367

    0.0065

    7.7032

    -0.0328

    0.0066

    6.1828

    chr3_18633152_A_C

    chr3_43656252_G_A

    0.0759

    0.01

    13.5747

    nan

    nan

    nan

    nan

    chr3_44176307_AAAG_A

    0.7812

    0.1679

    5.4822

    0.9816

    0.1974

    6.1793

    chr3_43656252_G_A

    chr3_158237129_A_G

    0.0388

    0.0065

    8.6487

    nan

    nan

    nan

    nan

    chr3_177171295_G_A

    0.0843

    0.0133

    9.588

    nan

    nan

    nan

    nan

    chr4_59388159_A_G

    -0.0403

    0.0071

    7.8402

    nan

    nan

    nan

    nan

    chr5_104451467_A_C

    0.0383

    0.0066

    8.1869

    nan

    nan

    nan

    nan

    chr5_120730291_A_G

    -0.0437

    0.0066

    10.5128

    nan

    nan

    nan

    nan

    chr5_121149217_A_C

    0.6199

    0.1257

    6.086

    0.7808

    0.1422

    7.3998

    chr5_120730291_A_G

    chr5_144466903_T_C

    0.0374

    0.0065

    8.1641

    nan

    nan

    nan

    nan

    chr5_153777668_A_C

    -0.0381

    0.0065

    8.3132

    nan

    nan

    nan

    nan

    chr5_153129992_T_G

    -0.0329

    0.0065

    6.3568

    -0.032

    0.0065

    6.0592

    chr5_153777668_A_C

    chr6_51715850_T_C

    -0.0567

    0.0103

    7.4145

    nan

    nan

    nan

    nan

    chr6_151880872_T_C

    -0.0474

    0.0065

    12.4306

    nan

    nan

    nan

    nan

    chr6_164751626_G_A

    -0.038

    0.0063

    8.717

    nan

    nan

    nan

    nan

    chr9_36999372_C_T

    0.0348

    0.0063

    7.419

    nan

    nan

    nan

    nan

    chr9_95537395_T_A

    0.0565

    0.0102

    7.4833

    nan

    nan

    nan

    nan

    chr10_21600368_A_AAC

    -0.0515

    0.0085

    8.819

    nan

    nan

    nan

    nan

    chr10_104842738_C_CT

    -0.0411

    0.007

    8.2919

    nan

    nan

    nan

    nan

    chr11_28582122_A_G

    -0.0389

    0.0066

    8.3234

    nan

    nan

    nan

    nan

    chr11_99647795_T_C

    0.0431

    0.0069

    9.5016

    nan

    nan

    nan

    nan

    chr11_113324873_A_G

    -0.038

    0.0064

    8.5837

    nan

    nan

    nan

    nan

    chr11_115118275_G_A

    -0.0407

    0.007

    8.312

    -0.0398

    0.007

    7.9104

    chr11_113324873_A_G

    chr11_113050349_C_T

    0.0364

    0.0064

    7.8798

    0.0331

    0.0064

    6.5628

    chr11_113324873_A_G,chr11_115118275_G_A

    chr12_60397384_T_A

    -0.0372

    0.0065

    8.0402

    nan

    nan

    nan

    nan

    chr14_70749996_T_C

    -0.227

    0.0359

    9.5829

    nan

    nan

    nan

    nan

    chr15_73812581_C_A

    -0.0584

    0.0105

    7.6144

    nan

    nan

    nan

    nan

    chr16_21667465_T_C

    0.0434

    0.0073

    8.6185

    nan

    nan

    nan

    nan

    chr16_65751219_A_G

    0.0357

    0.0064

    7.614

    nan

    nan

    nan

    nan

    chr16_72134342_T_G

    0.0485

    0.0063

    13.8185

    nan

    nan

    nan

    nan

    chr16_71324662_TCTGCTAATAGGAGTGA_T

    0.0829

    0.0128

    10.054

    0.0728

    0.0131

    7.582

    chr16_72134342_T_G

    chr18_53199573_T_C

    0.0497

    0.0063

    14.3777

    nan

    nan

    nan

    nan

    chr18_55212207_T_C

    0.0778

    0.0148

    6.843

    0.0759

    0.015

    6.3537

    chr18_53199573_T_C

    chr18_76052843_T_C

    0.0474

    0.0085

    7.6577

    nan

    nan

    nan

    nan

    chr19_49457409_G_T

    0.0795

    0.0136

    8.3038

    nan

    nan

    nan

    nan

    chrX_93697357_A_G

    0.4882

    0.0889

    7.3997

    nan

    nan

    nan

    nan

    chrX_93934138_A_G

    0.7061

    0.1479

    5.7454

    1.0262

    0.1883

    7.2998

    chrX_93697357_A_G

    chr3_18633152_A_C is the first hit to have a validit conditional chain with the secondary hit chr3_16811234_G_A, for which BETA, SE and MLOG10P are provided both for the original (input) sumstats and the conditioned one. In this case, one can see that the values did not change significantly after conditioning, but it can happen that variants go from being non significant to significant or that betas change considerably. Export to Sheets

  • all_logs. This file is simply the collection of all regenie outputs and it's meant for debugging in case something went wrong

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