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RefineComplexVariants

WDL source code

Refines complex SVs and translocations and filters based on discordant read pair and read depth evidence reassessment.

The following diagram illustrates the recommended invocation order:

Inputs​

info

All array inputs of batch data must match in order. For example, the order of the batch_name_list array should match that of batch_sample_lists, PE_metrics, etc.

vcf​

Input vcf, generated in CleanVcf.

prefix​

Prefix for output VCF, such as the cohort name. May be alphanumeric with underscores.

batch_name_list​

Array of batch names. These should be the same batch names used in GatherBatchEvidence.

batch_sample_lists​

Array of sample ID lists for all batches, generated in FilterBatch. Order must match batch_name_list.

PE_metrics​

Array of PE metrics files for all batches, generated in GatherBatchEvidence. Order must match batch_name_list.

Depth_DEL_beds, Depth_DUP_beds​

Arrays of raw DEL and DUP depth calls for all batches, generated in GatherBatchEvidence. Order must match batch_name_list.

n_per_split​

Shard size for parallel computations. Decreasing this parameter may help reduce run time.

Optional min_pe_cpx​

Default: 3. Minimum PE read count for complex variants (CPX).

Optional min_pe_ctx​

Default: 3. Minimum PE read count for translocations (CTX).

Optional use_hail​

Default: false. Use Hail for VCF concatenation. This should only be used for projects with over 50k samples. If enabled, the gcs_project must also be provided. Does not work on Terra.

Optional gcs_project​

Google Cloud project ID. Required only if enabling use_hail.

Outputs​

cpx_refined_vcf​

Output VCF.

cpx_evidences​

Supplementary output table of complex variant evidence.