small change in the shebang
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Removed a mistake
Updated the filtering step and the sample config to work with the latest samtools
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
update now that vr-login is our primary /software
run-filter: New config key "good_sites", plus renamed "fixed_filters" to "bad_sites".
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
LOH region caller for HipSci samples
run-filter: Index newly created BCF file
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Now integrated in to VRPipe::Steps::genome_studio_fcr_to_vcf
removed CONF override
removed CONF override
added support for new --species option
Runner: Make +verbose the default behaviour, +silent now gives the previous default. +verbose stays a hidden option.
vcf-merge: Reset -c before setting it
run-beagle: Added forgotten colon separator in FORMAT/DS output
removed hard-coding of CONF dir
run-filter: Fixed a typo, the command is "filter" not "filer"