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Various utility tools for working with genomics data
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amber explicit stringsAsFactors Nov 17, 2019
api-clients Made nct field optional in iclusion API Apr 16, 2019
bachelor Bachelor: added current config files Nov 18, 2019
bam-slicer Move code into sub-packages in hmf common Nov 13, 2019
count-bam-lines explicit stringsAsFactors Nov 17, 2019
ensembl-db Make ensembl db version dynamic Jul 22, 2019
fastq-stats Remove lots of initials from comments Jan 13, 2019
health-checker Move more code around Nov 13, 2019
hmf-common Functions can be package-private Nov 18, 2019
hmf-extensions Remove some unused code May 21, 2019
hmf-gene-panel-builder Remove initials from comments Jan 14, 2019
hmf-id-generator DEV-767: Refresh hashes for hmf sample IDs and bump version Nov 1, 2019
knowledgebase-importer Move code into sub-packages in hmf common Nov 13, 2019
patient-db DEV-964: add TODO message Nov 19, 2019
patient-reporter remove pathology tumor percentage from reports and remove PA report Nov 19, 2019
purity-ploidy-estimator Various minor code improvements in purple Nov 18, 2019
sage don't always realign Nov 16, 2019
sig_analyser Merge branch 'master' of https://github.com/hartwigmedical/hmftools Nov 18, 2019
stat_calcs Move more code around Nov 13, 2019
strelka-post-process Move reportable variant back into patient reporter Nov 14, 2019
sv-linx Merge branch 'master' of https://github.com/hartwigmedical/hmftools Nov 18, 2019
vicc-knowledgebase-importer DEV-759: Move json object creation into separate classes. Oct 3, 2019
.gitattributes add file attributes for shell scripts Aug 31, 2017
.gitignore Bumped patient db version Feb 13, 2018
LICENSE Bump license to GPLv3 Apr 15, 2019
README.md add Yourkit acknowledgement Oct 9, 2019
hmf_code_scheme.xml Disabled formatting of CSV files Apr 11, 2018
pom.xml Bump version of patient db Nov 15, 2019

README.md

hmftools

Various utility tools for working with genomics data

Resources used by HMF pipeline can be downloaded from https://resources.hartwigmedicalfoundation.nl

More detailed descriptions of the following algorithms are available from the links below:

Acknowledgement

Hartwig Medical Foundation uses the YourKit Java Profiler for Performance Tuning.

alt text

YourKit supports open source projects with innovative and intelligent tools for monitoring and profiling Java and .NET applications. YourKit is the creator of YourKit Java Profiler, YourKit .NET Profiler, YourKit YouMonitor.

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