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Last pushed: 3 months ago
Short Description
Commonly Used Programs for DNA-Seq Analysis
Full Description

Includes programs from cwarden45/genomics-base as well as:

cmake (v3.5.1)
pysam (v0.9.1.3)
biopython (v1.67)
gawk (v4.1.3)
VarScan2 (v2.4.2, /opt/VarScan.v2.4.2.jar)
GATK (v.3.6, /opt/GenomeAnalysisTK.jar)
Picard (v2.5, /opt/picard-tools-2.5.0/picard.jar)
LUMPY (v0.2.13, lumpy and lumpyexpress in /opt/lumpy-sv/bin)
GASVPro (v.1.2.1, in /opt/gasv/bin)
Pindel (v0.2.5b9, in /opt/pindel)
Manta (v1.0.0, /opt/manta-1.0.0.release_src/install/bin/configManta.py)
samblaster (v0.1.22, set in $PATH)
samtools (v1.3, set in $PATH)
bedtools (v2.25.0, /opt/bedtools2/bin/bedtools)
bcftools (v1.3.1, /opt/bcftools/bcftools)
HDF5 Libraries (in /opt/hdf5-1.8.17/hdf5)
CoNIFER (v0.2.2, /opt/conifer_v0.2.2/conifer.py)
DNAcopy (R Bioconductor package, v1.48.0)
SnpEff (v4.2, /opt/snpEff/snpEff.jar, includes GRCh37.75 database)
FastQC (v0.11.5, /opt/FastQC/fastqc)

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cwarden45