CallGenomicDisorderCNVs
Runs Bayesian copy-number variant inference at known genomic disorder loci using cohort-wide binned read-depth and
B-allele frequency data. This workflow operates as a standalone post-processing step after GatherBatchEvidence
completes, consuming the merged BAF and read-depth matrices. See the gatk-sv-gd repository for more information.
The following diagram illustrates the recommended invocation order:
Inputs
batch
An identifier for the batch; may only be alphanumeric with underscores.
baf_matrix
Path to the merged B-allele frequency matrix (TSV, gzipped) produced by GatherBatchEvidence. Must be indexed
(.tbi index file required at <baf_matrix>.tbi).
high_res_rd_matrix
Path to the merged high-resolution read-depth matrix (TSV, gzipped) produced by GatherBatchEvidence.
gd_table
Path to the genomic disorder regions table (TSV) defining known disorder loci with breakpoint annotations.
segdup_bed
Path to segmental duplication regions (BED) used for masking.
centromere_bed
Path to centromere regions (BED).
acrocentric_arm_bed
Path to acrocentric chromosome arm regions (BED).
custom_mask_bed
Path to custom masking regions (BED).
hard_inclusion_bed
Path to hard inclusion intervals (BED) that must be included in analysis regardless of other filters.
par_bed
Path to pseudoautosomal region intervals (BED).
gaps_bed
Path to assembly gap regions (BED).
gtf
Path to gene annotation file (GTF).
ploidy_table
Wide GATK-SV ploidy table (a sample column plus one column per contig), as produced by CreatePloidyTableFromPed. This must be the same table passed to IntegrateGDVcf: it is the authority on per-contig ploidy, and calls scored against any other ploidy cannot be encoded as GATK-SV genotypes. A sample/contig pair with ploidy 0 — the allosomes of a sex=0 sample, for example — is not genotypable, so no calls are emitted for it.
Optional flank_exclusion_intervals
Array of BED files defining intervals to exclude from flank analysis. Typically set to the same file as segdup_bed.
Optional rebinned_interval_size
Target interval size in base pairs for read-depth rebinning. Default: 10000.
Optional truth_table
Path to a truth set table for benchmarking.
Optional preprocess_args, infer_args, call_args, eval_args, plot_args
Free-form string arguments passed to the respective gatk-sv-gd subcommands.
Outputs
gd_output_tarball
Compressed tarball (.tar.gz) containing all GD analysis results, consumed by IntegrateGDVcf. See gatk-sv-gd for details about the tarball's contents.