| Deposited data |
|
| TCGA somatic mutation, copy |
Genomic Data Commons; |
https://gdc.cancer.gov/about-data/publications/pancanatlas |
| number, aneuploidy, genetic ancestry, |
(Campbell et al., 2016; |
|
| clinical data |
Carrot-Zhang et al., 2020) |
|
| COSMIC |
N/A |
https://cancer.sanger.ac.uk/cosmic |
| 1000 Genomes Project data |
(Auton et al., 2015) |
https://www.internationalgenome.org/ |
| ExAC |
(Karczewski et al., 2017) |
https://gnomad.broadinstitute.org/ |
| CIVic |
(Griffith et al., 2017) |
https://civicdb.org/home |
| UniProt |
(UniProt Consortium, 2019) |
https://www.uniprot.org/ |
| TCGA ATAC-seq data |
(Corces et al., 2018) |
https://gdc.cancer.gov/about-data/publications/ATACseq-AWG |
| TCGA normalized mRNA data |
Genomic Data Commons |
https://gdc.cancer.gov/about-data/publications/pancanatlas |
|
| Software and algorithms |
|
| BWA v0.6.2 |
(Li and Durbin, 2009) |
https://github.com/lh3/bwa |
| NovoSort v1.03.01 |
N/A |
http://www.novocraft.com/products/novosort/ |
| GATK v3.4 |
(McKenna et al., 2010) |
https://github.com/broadinstitute/gatk |
| MuTect v1.1.7 |
(Cibulskis et al., 2013) |
https://github.com/broadinstitute/mutect |
| Strelka v1.0.14 |
(Saunders et al., 2012) |
https://github.com/Illumina/strelka |
| LoFreq v2.1.3a |
(Wilm et al., 2012) |
https://csb5.github.io/lofreq/ |
| Pindel v0.2.5 |
(Ye et al., 2009) |
https://github.com/genome/pindel |
| Scalpel v0.5.3 |
(Narzisi et al., 2014) |
https://github.com/hanfang/scalpel-protocol |
| EBI validator v 0.4.3 |
N/A |
https://github.com/EBIvariation/vcf-validator |
| snpEff and snpSift |
(Cingolani et al., 2012a, 2012b) |
https://pcingola.github.io/SnpEff/ |
| Funseq2 |
(Fu et al., 2014) |
https://github.com/khuranalab/FunSeq2_DC |
| SignatureAnalyzer |
(Kim et al., 2016) |
https://github.com/broadinstitute/getzlab-SignatureAnalyzer |
| GISTIC 2.0 |
(Mermel et al., 2011) |
http://portals.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=216&p=t |
| Titan |
(Ha et al., 2014) |
https://github.com/gavinha/TitanCNA |
| SvABA |
(Wala et al., 2018) |
https://github.com/walaj/svaba |
| JaBbA |
(Hadi et al., 2020) |
https://github.com/shyiko/jabba |
| Circular Binary Segmentation |
(Olshen et al., 2004) |
|
| Sequenza |
(Favero et al., 2015) |
https://cran.r-project.org/web/packages/sequenza/index.html |
| Samtools |
(Li et al., 2009) |
https://github.com/samtools |
| gGnome |
(Hadi et al., 2020) |
https://github.com/mskilab/gGnome |
| SCISSOR |
(Choi et al., 2021) |
https://github.com/hyochoi/SCISSOR |
| fishHook |
(Imielinski et al., 2017) |
https://github.com/mskilab/fishHook |
