Skip to main content

ClusterBatch

WDL source code

Clusters SV calls across a batch. For each caller, redundant variants are merged across samples into representative variant records based on interval overlap criteria. Some variants will be hard-filtered if they overlap with predefined intervals known to pose challenges to SV and CNV callers (e.g. centromeres). GATK-SVCluster is the primary tool used in for variant clustering.

The following diagram illustrates the recommended invocation order:

note

GenerateBatchMetrics is the primary downstream module in batch processing. JoinRawCalls is required for genotype filtering but does not need to be run until later in the pipeline.

Inputs​

batch​

An identifier for the batch. Should match the name used in GatherBatchEvidence.

*_vcf_tar​

Standardized VCF tarballs from GatherBatchEvidence

del_bed, dup_bed​

Merged CNV call files (.bed.gz) from GatherBatchEvidence

ped_file​

Family structures and sex assignments determined in EvidenceQC. See PED file format.

Optional N_IQR_cutoff_plotting​

If provided, plot SV counts per sample. This number is used as the cutoff of interquartile range multiples for flagging outlier samples. Example value: 4.

Optional stripy_vcfs​

Single-sample STRipy VCFs to merge for the batch. In the Terra joint-calling workspace, these are produced by the optional standalone StripyWorkflow sample workflow and passed from the stripy_vcf sample attribute.

Outputs​

clustered_*_vcf​

Clustered variants for each caller (depth corresponds to depth-based CNV callers cnMOPS and GATK-gCNV) in VCF format.

Optional clustered_sv_counts, clustered_sv_count_plots, clustered_outlier_samples_preview, clustered_outlier_samples_with_reason, clustered_num_outlier_samples​

SV count QC tables and plots. Enable by providing N_IQR_cutoff_plotting

Optional merged_stripy_vcf, merged_stripy_vcf_index​

Batch-level merged STRipy VCF and index, present when stripy_vcfs is provided.