CNVpytor Track

The CNVpytor track (type = 'cnvpytor') is a tool for copy number analysis from read depth and B-allele frequency (BAF) of variants. As input, it takes BAM and/or VCF files. The analyzed data is stored in pytor file and can be viewed using cnvpytor track in igv. One can also use a whole genome VCF file as an input to the cnvpytor track. In such a case read depth and BAF information are calculated on-fly.

For details: https://github.com/abyzovlab/CNVpytor

File formats#

cnvpytor track can be loaded from either pytor or VCF files.

pytor#

• CNVpytor-produced pytor file.
• Option to switch among available bin sizes.
• Option to switch among available CNV callers.
• Signals:
  • Raw Read Depth
  • GC Corrected Read depth
  • CNV call
  • Maximum of BAF likelihood

vcf#

Whole genome VCF file with constraints.

• Indexed VCF files are not supported as data for the entire genome is required for the calculations.
• Both AD (Read Depth information) and GT (Genotype information) fields are required .
• Currently only a single genotype field is supported. Multi-sample VCFs are not supported.
• Currently, only ReadDepth CNV caller is available.
• Signals:
  • Raw Read Depth
  • Partition
  • CNV call
  • Maximum of BAF likelihood

Loading the data may take time, as it reads the entire VCF file and calculates the signals.

Configuration Options#

General options

Property	Description	Default
signal_name	Available Signal names rd_snp : Read Depth and BAF Likelihood rd : Read depth snp : BAF likelihood	rd_snp
cnv_caller	Name of CNV caller Options ReadDepth: Uses Read depth information only 2D: Uses both Read depth and BAF information Shows data based on available caller data.	2D
bin_size	Bin size pytor file: Bin size should be avialable in the pytor file vcf: Bin size should be multiple of 10,000	100000
colors	Color of the signals. Signal details are in file format section.	['gray', 'black', 'green', 'blue']

Examples#

pytor file as input#

{
    id: "pytor_track",
    type: "cnvpytor",
    name: "HepG2 pytor",
    url: "https://storage.googleapis.com/cnvpytor_data/HepG2_WGS.pytor",
}

View#

VCF file as input#

{
    id: "cnvpytor_track_vcf",
    type: "cnvpytor",
    name: "HepG2 VCF",
    url: "https://storage.googleapis.com/cnvpytor_data/HepG2.vcf.gz",
}

View#