Initial Commit
First test commit by Miika, including prospective license file.
Modified scripts to use /usr/bin/env instead of hard coded paths to Perl/R binaries. Fixed typos and indentation in vardict.pl.
Modified var2vcf_valid.pl, vardict.pl to use chr names from input bed file or command line
Generated symlink vardict to point to vardict.pl
Fixed teststrandbias.R var2vcf_valid.pl for empty input files (no variants)
Added option -E to exclude END-tags
Fixed a reference allele reporting bug
Somatic calling capability added for vardict.pl
Adding somatic capability for VarDict
Somatic testing R script added.
Drop Stat::Basic dependency for checkCov.pl
Fix the chromosome naming, added -C option so that it works for GRh37 chromosome naming.
var2vcf_somatic.pl var2vcf_valid.pl use chr names from samples. testsomatic.R test if input contains any lines.
Some updates.
update VCF convertion.
Updated with Miika's changes.
Somatic MSI updates
Updates
MSI added to var2vcf_somatic.pl