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IntegrateGDVcf

WDL source code

Integrates the genomic disorder (GD) CNV calls produced by CallGenomicDisorderCNVs into the cohort's filtered VCF. The workflow is scattered across chromosomes: the combined GD calls and per-batch ploidy tables are subset per contig and merged into the VCF using the gatk-sv-gd integrate CLI, then the per-contig VCFs are concatenated back into a single cohort VCF. See the gatk-sv-gd repository for more information.

The following diagram illustrates the recommended invocation order:

Inputs​

vcf​

Filtered VCF of the pipeline (cohort-level), and its index vcf_index.

prefix​

Prefix for the output VCF, such as the cohort name.

gd_output_tarballs​

Array of GD analysis tarballs, one per batch, produced by CallGenomicDisorderCNVs.

ploidy_tables​

Array of ploidy tables, one per batch, generated in GenerateBatchMetrics.

gd_table​

Path to the genomic disorder regions table (TSV), the same file used in CallGenomicDisorderCNVs.

par_bed​

Path to pseudoautosomal region intervals (BED).

contig_list​

List of contigs (one per line) to scatter the integration over.

Optional integrate_args​

Free-form string arguments passed to the gatk-sv-gd integrate subcommand.

Outputs​

integrate_gd_vcf​

Cohort VCF with genomic disorder CNV calls integrated.