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 thepheno
parameter.regenie_cond_sb.prefix
: the prefix of the outputregenie_cond_sb.pheno
: Phenotype name. It needs to match thesumstats_root
basenameregenie_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 notregenie_cond_sb.covariates
: List of covariates. The pipeline will filter them out to make sure only covaraites with >5 samples are includedregenie_cond_sb.chroms
: Comma separated list of chroms to include.regenie_cond_sb.regenie_conditional.max_steps
: Maximum number of iterations in the conditional analysisregenie_cond_sb.locus_mlogp_threshold
: Mlogp threshold for the initial hitregenie_cond_sb.conditioning_mlogp_threshold
: Mlogp threshold for the conditioned hitThese 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.VARIANTBETASEMLOG10PBETA_condSE_condMLOG10P_condVARIANT_condchr1_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 hitchr3_16811234_G_A
, for whichBETA
,SE
andMLOG10P
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 Sheetsall_logs
. This file is simply the collection of all regenie outputs and it's meant for debugging in case something went wrong
Last updated
Was this helpful?