vcffilter now supports indels, new indel metrics in vcfcheck
Allow single BAM file on input, do not require it to be listed in a file of file names
Check for maximum LSF job length
More informative error message when duplicate job names detected
Support for indels
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
vcfcheck: Changed output format of Ts/Tv
VCF csq support scripts
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Check exit status of matplotlib in plot_randomize
Added --haplotype option
plot-vcfcheck: Produce the overlap by AF graphs
Do not use all annotations to initialize distributions, some may be faulty
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
vcf to dbsnp format script
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
check max var length by comparing ref and allele lengths
Summary commit of several important changes, new features and bugfixes in vcffilter, vcfcheck, vcfnorm and other tools.
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Reflect changes in vcfcheck and vcffilter