VarScan2seqz

a data frame from the output file of <code class="command">somatic</code>.

varscan.somatic

a data frame from the output file of <code class="command">copynumber</code> (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 <code class="command">somatic</code> and <code class="command">copynumber</code> programs, which are part of VarScan version 2. The resulting object can be used, in lieu of a &#8220;seqz&#8221; 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.

Francesco Favero

sequenza

Copy Number Estimation from Tumor Genome Sequencing Data

VarScan2seqz function

a data frame from the output file of <code class='command'>somatic</code>.

a data frame from the output file of <code class='command'>copynumber</code> (optional).

This function reads the output files from the <code class='command'>somatic</code> and <code class='command'>copynumber</code> programs, which are part of VarScan version 2. The resulting object can be used, in lieu of a &#8220;seqz&#8221; object, within Sequenza.

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

Description

Usage

Arguments

Value

Details

References