| Critical commercial assays |
|
| QIAamp DNA Mini Kit |
Qiagen, Germany |
Cat#51304 |
| DNA Blood Midi Kit |
Qiagen, Germany |
Cat#51183 |
| MGIeasy Exome Capture V4 probe set |
MGI Tech Co., Ltd, China) |
Cat#1000007745 |
|
| Deposited data |
|
| Raw and analyzed data |
This paper |
CNSA: CNP0000594 |
| Human reference genome NCBI build 37, GRCh37 |
Genome Reference Consortium |
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| COSMIC |
Forbes et al., 2015 |
https://cancer.sanger.ac.uk/cosmic/ |
|
| Software and algorithms |
|
| SOAPnuke (v1.5.6) |
Chen et al., 2018 |
https://github.com/BGI-flexlab/SOAPnuke |
| BWA-MEM (v0.7.12) |
Li et al., 2009 |
http://bio-bwa.sourceforge.net/ |
| Picard (v1.137) |
Broad Institute |
https://broadinstitute.github.io/picard/ |
| Genomic Analysis Toolkit (GATK v3.8.0) |
McKenna et al., 2010 |
https://software.broadinstitute.org/gatk/ |
| BAM-matcher |
Wang et al., 2016 |
https://bitbucket.org/sacgf/bam-matcher/src/master/ |
| SAMtools (v1.2) |
Li et al., 2009 |
http://samtools.sourceforge.net/ |
| VarScan 2 (v2.4.3) |
Koboldt et al., 2012 |
http://dkoboldt.github.io/varscan/ |
| MuTect (v1.1.7) |
Cibulskis et al., 2013 |
https://github.com/broadinstitute/mutect |
| ANNOVAR |
Wang et al., 2010 |
http://annovar.openbioinformatics.org/en/latest/ |
| PyClone (v0.13.1) |
Roth et al., 2014 |
https://github.com/aroth85/pyclone |
| Sequenza (v3.0.0) |
Favero et al., 2015 |
https://bitbucket.org/sequenzatools/sequenza/src/master/ |
| Copynumber (v1.24.0) |
Nilsen et al., 2012 |
https://bioconductor.org/packages/release/bioc/html/copynumber.html |
| CITUP (v0.1.0) |
Malikic et al., 2015 |
https://github.com/sfu-compbio/citup |
| MapScape (v1.8.0) |
Smith et al., 2017 |
https://bioconductor.org/packages/release/bioc/vignettes/mapscape/inst/doc/mapscape_vignette.html |
| REVOLVER (v0.2.0) |
Caravagna et al., 2018 |
https://github.com/caravagn/revolver |
| PHYLIP (v3.697) |
Falenstein, 1989 |
http://evolution.genetics.washington.edu/phylip.html |
| FigTree (v1.4.4) |
Rambaut, 2007 |
http://tree.bio.ed.ac.uk/software/figtree/ |
| DeconstructSigs (v1.8.0) |
Rosenthal et al., 2016 |
https://github.com/raerose01/deconstructSigs |
| Platypus (v0.8.1) |
Rimmer et al., 2014 |
https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data |
| RECUR |
Jakubek et al., 2019 |
https://gitlab.com/permutations/recur |
|
| Other |
|
| Sequence data, analyses, and resources related to the high depths multiregional sequencing of colorectal cancer |
This paper |
N/A |
