Sequenza-utils

Sequenza-utils is The supporting python library for the sequenza R package.

Sequenza is a software for the estimation and quantification of purity/ploidy and copy number alteration in sequencing experiments of tumor samples. Sequenza-utils provide command lines programs to transform common NGS file format - such as BAM, pileup and VCF - to input files for the R package

User documentation

• Installation
  • Latest release via PyPI
  • Development version
• Command line interface
  • CG wiggle
  • BAM/mpileup to seqz
  • Binning seqz
  • VCF to seqz
  • Merge overlapping seqz
• User cookbook
  • Generate GC reference file
  • From BAM files
  • Binning seqz, reduce memory
  • Seqz from VCF files
  • Merge seqz files

Library reference

• API library interface
  • sequenza.izip
  • sequenza.wig
  • sequenza.fasta
  • sequenza.pileup
  • sequenza.samtools
  • sequenza.seqz
  • sequenza.vcf