GenerateBatchMetrics
Analyzes variants for RD, BAF, PE, and SR evidence and creates a table of metrics containing raw and statistical
metrics. These results are used to assess variant quality in FilterBatch and for SR-based breakpoint refinement.
Modified tests are applied to common variants (carrier frequency at least 50%) and results are emitted in a separate table.
The following diagram illustrates the recommended invocation order:
Inputs
batch
An identifier for the batch. Should match the name used in GatherBatchEvidence.
*_vcf
Clustered VCFs from ClusterBatch.
baf_file
Merged BAF evidence file from GatherBatchEvidence.
pe_file
Merged PE evidence file from GatherBatchEvidence.
rd_file
Merged RD evidence file from GatherBatchEvidence.
sr_file
Merged SR evidence file from GatherBatchEvidence.
median_file
Merged median coverage table from GatherBatchEvidence.
ped_file
Family structures and sex assignments determined in EvidenceQC. See PED file format.
records_per_shard_agg
Variants per shard for evidence testing. Reduce defaults to increase parallelism if the workflow is too slow.
Optional outlier_sample_ids
Provide a file containing sample IDs, delimited by new lines, to exclude from the generation of batch metrics - this should be based on outlier samples identified following EvidenceQC that are still retained in the cohort. If provided, the workflow discards any outlier samples from being considered as part of the called samples when calculating metrics at a given site, as long as non-outlier samples are also called for that site. It does the same for the set of background samples considered in the metric calculations for a given site. These outlier samples are not removed from joint calling in downstream modules.
Outputs
metrics
TSV of variant metrics
ploidy_table
TSV of contig ploidies for all samples, assuming diploid autosome and sex assignments from the ped_file.