Use /software/vertres/lib/R-2.15.2/ as PluriTest does not work with R version 3
Use /software/vertres/lib/R-2.15.2/ as PluriTest does not work with R version 3
latest bcftools has changed the -o option to -O
genome_studio_import_from_irods pipeline replaced with genome_studio_import_from_irods_and_convert_to_vcf pipeline featuring new illumina_coreexome_manifest_to_map step and updated genome_studio_fcr_to_vcf step that both use fcr-to-vcf
genome_studio_import_from_irods pipeline replaced with genome_studio_import_from_irods_and_convert_to_vcf pipeline featuring new illumina_coreexome_manifest_to_map step and updated genome_studio_fcr_to_vcf step that both use fcr-to-vcf
moved penncnv tests to the the genome_studio_import_and_genotype_comparison.t script
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
replaced hard-coded local paths with env vars
added support for arbitrary filetypes