Pinned Repositories
barclay
Command line argument parser and online documentation generation utilities for java command line programs.
gatk
Official code repository for GATK versions 4 and up
gatk-bwamem-jni
JNI code for bwa mem
gatk-native-bindings
GATK Native Bindings Repository
jopt-simple
Java library for parsing command line options
variant-to-igv
A tool which takes a variant file and bams, and creates igv screenshots of each of the variants.
htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
lbergelson's Repositories
lbergelson/grgit
The Groovy way to use Git.
lbergelson/maftools
Python convenience functions for working with mutation annotation format files (MAF)
lbergelson/gamgee
A C++ interface for NGS data formats
lbergelson/travis_test
lbergelson/coveralls-python
Show coverage stats online via coveralls.io
lbergelson/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
lbergelson/somatic-benchmark
Tools for comparing somatic variant calling tools.
lbergelson/optparse
R package proving commandline optional argument parser
lbergelson/practice
lbergelson/misc
miscellaneous scripts
lbergelson/variant-to-igv
A tool which takes a variant file and bams, and creates igv screenshots of each of the variants.
lbergelson/PanelOfNormalsFilter
Filtering a somatic variant file against a panel of normal variants.
lbergelson/mutect
MuTect -- Accurate and sensitive cancer mutation detection
lbergelson/VCFcomparator
Tool for comparing mutation calls in VCF format
lbergelson/gatk
GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses
lbergelson/git
Git Source Code Mirror - This is a publish-only repository and all pull requests are ignored. Please follow Documentation/SubmittingPatches procedure for any of your improvements.
lbergelson/git-aware-prompt
Display current Git branch name in your terminal prompt when in a Git working directory.