CaMutQC-v0.99.2

What's Changed

• IMPORTANT: PON files are removed from this repo and this package, please provide PON file when running mutFilterPON function. You can download it from GATK. Ref: https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON
• Standardization of data files, update logo by @Wangxin555 in #36
• Update calTMB so users can use own bed file with assay by @Wangxin555 in #37
• Add PONfile, verbose parameters by @Wangxin555 in #38

Full Changelog: CaMutQC-v.0.99.0...CaMutQC-v0.99.2

CaMutQC-v0.99.0

A stable version, ready to be checked by Bioconductor.
Future releases with updates during the reviewing process will be under this tag.

CaMutQC-v0.10.0

New features!

• Read VCFs from multi-caller directly! Files should under the same location
• Add information about parameter set sharing in the manual and function annotation. Try now and contribute to the community!

CaMutQC-v0.9.0

Faster, more accurate, more stable!!

• Update License to GPL-v3
• Take more corner cases into consideration when selecting transcripts
• Add progress bar
• Improve efficiency when filtering

CaMutQC-v0.8.0

Now CaMutQC is able to read VCF files from VarScan2, MuTect2 and MuSE, and filter variants without any bugs!!

• Some default parameters are modified to provide a more flexible filtering experience.
• Filtering efficiency has been greatly improved.

CaMutQC-v0.7.0

Fix some essential bugs and improve efficiency

This release:

1. fix bugs in mutFilterAdj function, enabling user to filter somatic mutations for SNV-only or INDEL-only vcfs
2. improve running efficiency by removing some for loop, use merge, mutate instead
3. update the manual

CaMutQC-v0.6.0

The development of CaMutQC is back on track!

This release:

• Was tested using devtools on R-4.3.1 under Windows 10 x64.
• Reorganized inst/extdata folder and updated reference info about external datasets.
• Carried with standardized manual and configuration.

CaMutQC-v0.5.0

• Provide more options for mutFilterQual function, including 'WES', 'MSKCC' and 'Customized'
• Move mutFilterPON and mutFilterNormalDP from mutSelection to mutFilterTech
• Update manual
• Update README

CaMutQC-v0.4.0

• Add mutFilterRef function for reference-based filtration
• Update manual and filter report
• Code reorganization
• Update workflow
• Fix some bugs

CaMutQC-v0.2.0

CaMutQC v0.2.0 updates in the following aspects:

• Change parameter COSMIConly to keepCOSMIC, for keeping COSMIC mutations while they are in other databases but not only keeping COSMIC mutations.
• Add function processMut, which can take union/intersection on mutations from multiple MAF data frames.
• Modify related files including manual, workflow, README, etc.

PS: Happy New Year!!