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CombineBatches

WDL source code

Merges variants across multiple batches. Variant merging uses similar methods and criteria as in ClusterBatch, but in addition requires samples genotyped as non-reference to match sufficiently.

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 pesr_vcfs, depth_vcfs, etc.

cohort_name​

Cohort name. The guidelines outlined in the sample ID requirements section apply here.

batches​

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

Optional merge_vcfs​

Default: false. If true, merge contig-sharded VCFs into one genome-wide VCF. This may be used for convenience but cannot be used with downstream workflows.

pesr_vcfs​

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

depth_vcfs​

Array of re-genotyped depth caller variants for all batches, generated in RegenotypeCNVs.

raw_sr_bothside_pass_files​

Array of variant lists with bothside SR support for all batches, generated in GenotypeBatch.

raw_sr_background_fail_files​

Array of variant lists with low SR signal-to-noise ratio for all batches, generated in GenotypeBatch.

localize_shard_size​

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

min_sr_background_fail_batches​

Threshold fraction of batches with high SR background for a given variant required in order to assign this HIGH_SR_BACKGROUND flag. Most users should leave this at the default value.

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​

combined_vcfs​

Array of contig-sharded VCFs of combined PE/SR and depth calls.

cluster_bothside_pass_lists​

Array of contig-sharded bothside SR support variant lists.

cluster_background_fail_lists​

Array of contig-sharded high SR background variant lists.

combine_batches_merged_vcf​

Genome-wide VCF of combined PE/SR and depth calls. Only generated if using merge_vcfs.