Description

Calls germline copy number variants (CNVs) from whole genome sequencing data using Illumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this mode is recommended for single germline samples as well as small pedigrees. The module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy information, and outputs a VCF with copy number status across the genome together with a coverage-and-variant-frequency file used for downstream segmentation.

Input

Name
Description
Pattern

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germline_snv_vcf (file)

VCF (or gzipped VCF) containing germline SNV b-allele sites (PASS filter only). Typically produced by a variant caller such as DNAscope or DeepVariant.

*.{vcf,vcf.gz}

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genomedir (directory)

Canvas genome reference directory containing genome.fa and GenomeSize.xml. Available for GRCh37/hg19/GRCh38 from s3://canvas-cnv-public.

reference (file)

Canvas-ready kmer reference file (kmer.fa). Available from s3://canvas-cnv-public.

*.fa

filter13 (file)

BED file of regions to exclude from CNV calling (e.g. centromeres, telomeres). Named filter13 following Canvas reference package conventions. Available from s3://canvas-cnv-public.

*.bed

Output

Name
Description
Pattern

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Tools

canvas Documentation

Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data.

https://github.com/Illumina/canvasLicense: GPL-3.0
Authors