VarScan2seqz

a data frame from the output file of <command>somatic.

varscan.somatic

a data frame from the output file of <command>copynumber (optional).

varscan.copynumber

defines the variant allele frequency threshold on the normal genotype to filter out false positive heterozygous position.

normal_var_freq

This function reads the output files from the <command>somatic and <command>copynumber programs, which are part of VarScan version 2. The resulting object can be used, in lieu of a <dquote>seqz</dquote> object, within Sequenza.

Tools to analyze genomic sequencing data from
 paired normal-tumor samples, including cellularity and ploidy estimation; mutation
 and copy number (allele-specific and total copy number) detection, quantification 
 and visualization.

VarScan2seqz: Import VarScan output files, for use with the Sequenza algorithm.

Description

Usage

Arguments

Value

Details

References