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title: Cancer Genomics Tools & Resources
tags: [Resources, Tools, Cancer, Genomics]

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title: 'Cancer Genomics Tools & Resources'
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Cancer Genomics Tools & Resources
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## Table of Contents

[TOC]

## README

This is a living document where you can add tools & resources (TR) that we should take a look at and discuss as options for any part of the bioinformatics processing or analysis of cancer samples.

There will probably, and hopefully, be a lot of changes to this document early on.

**How to add something:**
1. If the topic section already exists, add a link to your TR. If the topic section does not exist, create it!
2. If available, also add the article about the TR and any good benchmarking resource.
3. Finally, add a brief description about the resource. This can include:
    3a. What the tool/resource is.
    3b. When it should be used.


Tools
===

Somatic Variant Calling
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### Mutect2

Somatic variant caller in GATK. Useful for detecting low frequency variants.
**Link:** https://github.com/broadinstitute/gatk/releases
**Article:** https://www.biorxiv.org/content/10.1101/861054v1
**Guide:** https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2
**Benchmark** (against other tools): https://www.nature.com/articles/s41598-020-60559-5

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Copy number variation
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### PureCN
### CNVkit
Article: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004873
Link: https://cnvkit.readthedocs.io/en/stable/
### ASCAT
Estimates somatic copy number aberrations, tumor purity and tumor ploidy using LogR and BAF data. ASCAT 3.0 recently released, has multi-sample version.
Article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8317109/
Link: https://github.com/VanLoo-lab/ascat

Annotation
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Resources
===

Annotation
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### CIViC
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
**Link:** https://civicdb.org/releases/main
**Article:** https://www.nature.com/articles/ng.3774

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Reference genomes
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###### tags: `Cancer` `Tools` `Resources` `Genomics`
