VisualizeCnvs
Generates plots of read depth across all samples. This is useful for visualizing large deletions and duplications (at least 5kbp).
This module is not a part of the core pipeline but may be used to investigate variants of interest.
Inputs
All array inputs of batch data must match in order. In particular, the ordering of median_files and rd_files must
be the same.
vcf_or_bed
VCF or bed file containing variants to plot. All variants will be automatically subsetted to DEL and DUP types subject
to the min_size constraint. VCF files must end in .vcf.gz and bed files must end in either .bed or
.bed.gz. Bed files must contain columns: chrom,start,end,name,svtype,samples.
prefix
Output prefix, such as cohort name. May be alphanumeric with underscores.
median_files
Array of median coverage files for all batches in the input variants, generated in GatherBatchEvidence.
rd_files
Array of RD evidence files for all batches in the input variants, generated in GatherBatchEvidence.
ped_file
Family structures and sex assignments determined in EvidenceQC. See PED file format.
min_size
Minimum size in bases of variants to plot.
flags
Additional flags to pass to the RdTest plotting script.
Due to a bug, the flags parameter must contain -s 999999999 in order to properly plot variants over 1 Mb.
Outputs
rdtest_plots
Tarball containing output plots.