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JoinRawCalls

WDL source code

This module clusters raw unfiltered variants from ClusterBatch across all batches. Concordance between these genotypes and the joint call set usually can be indicative of variant quality and is used downstream for genotype filtering.

The following diagram illustrates the recommended invocation order:

Inputs​

prefix​

Prefix for the output VCF, such as the cohort name. The guidelines outlined in the sample ID requirements section apply here.

clustered_*_vcfs​

Array of clustered VCFs for all batches, generated in ClusterBatch.

ped_file​

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

Outputs​

joined_raw_calls_vcf​

VCF containing all raw calls in the cohort.

ploidy_table​

TSV of contig ploidies for all samples, assuming diploid autosome and sex assignments from the ped_file.