CaMutQC - 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 https://github.com/likelet/CaMutQC/pull/36
• Update calTMB so users can use own bed file with assay by @Wangxin555 in https://github.com/likelet/CaMutQC/pull/37
• Add PONfile, verbose parameters by @Wangxin555 in https://github.com/likelet/CaMutQC/pull/38

Full Changelog: https://github.com/likelet/CaMutQC/compare/CaMutQC-v.0.99.0...CaMutQC-v0.99.2

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Published by Wangxin555 over 2 years ago

CaMutQC - 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.

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Published by Wangxin555 over 2 years ago

CaMutQC - 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!

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Published by Wangxin555 over 2 years ago

CaMutQC - 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

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Published by Wangxin555 over 2 years ago

CaMutQC - 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.

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Published by Wangxin555 over 2 years ago

CaMutQC - 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

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Published by Wangxin555 almost 3 years ago

CaMutQC - 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.

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Published by Wangxin555 almost 3 years ago

CaMutQC - 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

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Published by Wangxin555 almost 4 years ago

CaMutQC - CaMutQC-v0.4.0

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

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Published by Wangxin555 over 4 years ago

CaMutQC - 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!!

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Published by Wangxin555 over 4 years ago