Conditional Analysis with custom regions and loci

How to run conditional analysis with custom region and loci

Description

It is possible now to run a simplified version of the conditional analysis that allows to pass:

• a custom list of regions

• a list of loci to start the conditioning from

20 48818241-54558868 chr20_50318241_A_G,chr20_53058868_G_A
14 80620000-81150000 chr14_81006112_T_A

In this scenario two shards will be created. One for each region and in the first region the conditioning will start from a joint conditioning over the two variants and proceed as per usual with a chain until the desired threshold is reached

Input files

The procedure for submission is similar to Conditional analysis. The most important inputs are" - cond_regions : a file with the list of regions and loci as shown above - pheno name of phenotype - null path to step1 regenie null The modifiable wdl and json can be found at finngen/library-green/scripts/conditional/regenie_cond_region.sb.*

Submit your job

Once your inputs are in order, you can submit your job via command line:

finngen-cli request-workflow \\
--wdl /path/to/conditional_analysis_custom.wdl \
--input /path/to/conditional_analysis_custom.json

REMEMBER to save your job ID [WORKFLOW_ID]to keep track of your job and to be able to view the output! See also tips on how to find a pipeline job ID. The [WORKFLOW_ID] and your job can be monitored from the pipelines.

A version of this pipeline is also available as an unmodifiable pipeline