cwarden45/dnaseq-dependencies repository overview

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 (v4.0.1.1, wrapper is /opt/gatk-4.0.1.1/gatk) 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)