Merge branch 'master' of github.com:cc0qe/speedseq
report somatic scores (SSC) for somatic variants
fixed SSC_THRES variable for filtering
updated SSC formula and thresholds
updated command line help
automatically create PED file for somatic module
reordered installation items
fixed make
bump version
Merge branch 'master' of github.com:cc2qe/speedseq
fixed bug in re-align that wouldn't properly source GNU parallel
changed to realign
readgroup in renamed read names
speedseq realign: auto-detect libraries in BAM and align them separately. optionally, merge them into a single BAM at the end
quiet mbuffer, don't generate extraneous pre-merge BAM indices in realign
bump svtyper version (bugfix in genotyping non-N-padded contigs, like EBV)
Update README.md
When defining the library insert size distribution for LUMPY, ignore the proper pair flag from BWA, as this biases the distribution to BWA's definition of a proper pair
Merge branch 'master' of github.com:cc1qe/speedseq
bug fix: VEP wasn't working with 1 thread (--fork flag)