Skip to main content

RegenotypeCNVs

WDL source code

Re-genotypes probable mosaic variants across multiple batches. This is a "cohort-level" workflow that operates on all batches.

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 batches array should match that of depth_vcfs, batch_depth_vcfs, etc.

depth_vcfs​

Array of genotyped depth caller variants for all batches, generated in GenotypeBatch.

cohort_depth_vcf​

Merged depth caller variants for the cohort, generated in MergeBatchSites.

batch_depth_vcfs​

Array of filtered depth caller variants for all batches, generated in FilterBatch. Order must match that of depth_vcfs.

coveragefiles​

Array of merged RD evidence files for all batches from GatherBatchEvidence. Order must match that of depth_vcfs.

medianfiles​

Array of median coverage tables for all batches from GatherBatchEvidence. Order must match that of depth_vcfs.

RD_depth_sepcutoffs​

Array of "depth_depth" genotype cutoff files (depth evidence for depth-based calls) generated in GenotypeBatch. Order must match that of depth_vcfs.

n_per_split​

Records per shard when scattering variants. Decrease to increase parallelism if the workflow is running slowly.

n_RD_genotype_bins​

Number of depth genotyping bins. Most users should leave this at the default value.

batches​

Array of batch identifiers. Should match the name used in GatherBatchEvidence. Order must match that of depth_vcfs.

cohort​

Cohort name. May be alphanumeric with underscores.

regeno_coverage_medians​

Array of regenotyping metrics generated in GenotypeBatch.

Outputs​

regenotyped_depth_vcfs​

Array of batch depth VCFs after regenotyping.