Germline Build WGS gCNV Model

Implementation of the helper_gcnv_model_wgs step

The helper_gcnv_model_wgs step takes as the input the results of the ngs_mapping step (aligned germline reads) and builds a model that can be used by GATK4 gCNV. Important: the workflow assumes that all samples in the cohort use the same library kit and all are WGS.

Step Input

The step uses Snakemake sub workflows for the result of the ngs_mapping (aligned reads BAM files).

Step Output

All donors will be used to generate the two parts of the required gCNV model, specifically: ploidy-model and cnv_calls-model. Both are required to execute gCNV in CASE mode.

For example, the relevant directories might look as follows:

work/
+-- bwa.gcnv_contig_ploidy.default
    `-- out
        `-- bwa.gcnv_contig_ploidy.default
            |-- SAMPLE_0
            |   |-- contig_ploidy.tsv
            |   |-- global_read_depth.tsv
            |   |-- mu_psi_s_log__.tsv
            |   |-- sample_name.txt
            |   `-- std_psi_s_log__.tsv
            |-- [...]
            `-- bwa.gcnv_contig_ploidy.default
                `-- ploidy-model
                    |-- contig_ploidy_prior.tsv
                    |-- gcnvkernel_version.json
                    |-- interval_list.tsv
                    |-- mu_mean_bias_j_lowerbound__.tsv
                    |-- mu_psi_j_log__.tsv
                    |-- ploidy_config.json
                    |-- std_mean_bias_j_lowerbound__.tsv
                    `-- std_psi_j_log__.tsv
+-- bwa.gcnv_call_cnvs.default.***_of_***
    `-- out
        `-- bwa.gcnv_call_cnvs.default.***_of_***
            |-- cnv_calls-calls
            |   |-- SAMPLE_0
            |       `-- [...]
            |   |-- [...]
            |-- cnv_calls-model
            |  |-- denoising_config.json
            |  |-- gcnvkernel_version.json
            |  |-- interval_list.tsv
            |  |-- log_q_tau_tk.tsv
            |  |-- mu_W_tu.tsv
            |  |-- mu_ard_u_log__.tsv
            |  |-- mu_log_mean_bias_t.tsv
            |  |-- mu_psi_t_log__.tsv
            |  |-- std_W_tu.tsv
            |  |-- std_ard_u_log__.tsv
            |  |-- std_log_mean_bias_t.tsv
            |  `-- std_psi_t_log__.tsv
            `-- cnv_calls-tracking
                `-- [...]

Global Configuration

• At the moment, no global configuration is used.

Default Configuration

The default configuration is as follows.

# Default configuration helper_gcnv_model_wgs
step_config:
  helper_gcnv_model_wgs:
    path_ngs_mapping: ../ngs_mapping  # REQUIRED

    gcnv:
      # Path to BED file with uniquely mappable regions.
      path_uniquely_mapable_bed: null  # REQUIRED