Copy Number Estimation from Tumor Genome Sequencing Data
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
Changes in version 3.0.0 (2019-05-09)
- Code cleanup and refactoring
- Bug fixes
- Use readr and stop relying on system commands (grep, sed, gunzip) to read seqz files
- Use the package pbapply for progress bar
- Normalize each sample separately
- Provide coverage profile of the 2 samples separately, before and after normalization
- Provide CG-content vs depth profile for each samples, before and after normalization
- Draw standard "mirrored" BAF (from 0 to 1) in the raw genome view
Changes in version 2.1.2 (2015-08-18)
- Keep the order of the bases corresponding to the major and minor alleles as in the normal sample. (allows mocking haplotype).
- Fix check for NOTES in newer R versions
Changes in version 2.1.1 (2015-01-20)
- Fix heterozygous detection when importing VarScan2 data of very high coverage seq.
- Cleanup sequenza-utils.py
- Update citation info to published manuscript
Changes in version 2.1.0 (2014-10-08)
- Add sequenza-utils.py function bam2seqz
- Add raw data depth-ratio/Bf in the genome view plots
- Results model fitting plot using the B-allele/depth-ratio plot.
- Present alternative solutions using local maxima of the CP plot.
- Model the expected B-allele frequencies with a t-distribution using the observed sd, rather then taking the 95% of the observed Bf.
- Use dt instead of dbinom for the BAF and depth ratio model.
- Fix documentation discrepancies on the sequenza-utils.py execution.
- Add breaks as optional argument - enables to input custom segmentation -
- Add different segmentation options, fast, het and full, corresponding to different resolutions.
- Minor fixes.
Changes in version 2.0.0 (2014-04-08)
- Change seqz names header and some function arguments/formats to improve usability
- Add to sequenza.fit a method argument to calculate cellularity and ploidy also from mutations
- Change the recommended file extension from ".abfreq" to ".seqz" for clarity.
- The "seqz" file now contains a column with strand orientation information.
- "cp.plot" now plots the scaled log-likelihood.
- "theoretical.depth.ratio" now implements the correct formula.
- The "theoretical.*" functions have their arguments rearranged, and defaults changed, for consistency.
- "sequenza.extract" now has additional filtering arguments.
- Miscellaneous cleanup/simplification/optimization.
Changes in version 1.0.5 (2014-02-04)
- Add a python utility for binning the data to a desired window size (reducing vastly memory footprint in the analysis)
- Fix default workflows parameter to detect CN up to 20.
Changes in version 1.0.4 (2014-01-16)
- Add function to import VarScan2 output
- Add results function, to save results and standard plots.
- Fix error on loading non-zipped files in the workflow.
- Ignore error and finish the process if one of the chromosome fails in the workflows.
Changes in version 1.0.3 (2013-12-12)
- Fix grep instructions that broke single chromosome loading