somatic can handle multiple bams
cleaned up help
added multiple library support
Merge branch 'local' of github.com:cc2qe/speedseq into local
fixed argument parsing for somatic
updated var module to use VEP instead of SnpEff. currently slow though, because spools up one VEP instance for each freebayes thread. Plan to run forked VEP on whole file in next commit
ought to be faster VEP annotation
added threads for VEP
fixed verbose typo
use VEP for somatic as well
forgot a backslash
switched pairend_distro to python implementation
changed error-checking executables for VEP instead of SnpEff
added hall-lab/sv-tools submodule
added sv cnv and genotyping tools
lumpy outputs VCF, allows keeping temporary files
LUMPY vcf is now genotyped in parallel
added basic genotyping and CNV functionality
these are intense debugging versions of svgt and getmate for timings. to be stashed and deleted.
remove get mate