C# Class CanvasSNV.SNVReviewer

The SNV reviewer takes as input a .vcf file (from the normal sample) and a .bam file (from the paired tumor sample). It processes a particular chromosome at a time. For all variants in the .vcf file that pass our filters, we review the variant allele frequency in the .bam file from the tumor sample. We output that data in tabular format.

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Protected Properties

Property	Type	Description
BamPath	string
Chromosome	string
MinimumMapQ	int
OutputPath	string
VcfPath	string

Public Methods

Method	Description
Run ( ) : int
SNVReviewer ( string chromosome, string vcfPath, string bamPath, string outputPath, int minMapQ ) : System

Protected Methods

Method	Description
LoadVariants ( string vcfPath ) : void	Step 1: Load the normal het SNVs of interest.
ProcessBamFile ( string bamPath ) : void	Step 2: Get the ref and variant allele frequencies for the variants of interest, in the tumor bam file.
WriteResults ( string outputPath ) : void	Step 3: Summarize results to a simple tab-delimited file.

Private Methods

Method	Description
ProcessReadBases ( BamAlignment read, int nextVariantIndex ) : void	Use the CIGAR string to map bases to chromosome positions, and check whether we see the ref base or the variant allele for our variants of interest.

Method Details

LoadVariants() protected method

Step 1: Load the normal het SNVs of interest.

protected LoadVariants ( string vcfPath ) : void
vcfPath	string
return	void

ProcessBamFile() protected method

Step 2: Get the ref and variant allele frequencies for the variants of interest, in the tumor bam file.

protected ProcessBamFile ( string bamPath ) : void
bamPath	string
return	void

Run() public method

public Run ( ) : int
return	int

SNVReviewer() public method

public SNVReviewer ( string chromosome, string vcfPath, string bamPath, string outputPath, int minMapQ ) : System
chromosome	string
vcfPath	string
bamPath	string
outputPath	string
minMapQ	int
return	System

WriteResults() protected method

Step 3: Summarize results to a simple tab-delimited file.

protected WriteResults ( string outputPath ) : void
outputPath	string
return	void

Property Details

BamPath protected_oe property

protected string BamPath
return	string

Chromosome protected_oe property

protected string Chromosome
return	string

MinimumMapQ protected_oe property

protected int MinimumMapQ
return	int

OutputPath protected_oe property

protected string OutputPath
return	string

VcfPath protected_oe property

protected string VcfPath
return	string