Add REJECT filter to non-somatic records in VarScan2

Like the work done in FreeBayes, this patch adds a REJECT filter to
non-somatic records (i.e., everything with a Somatic Status - SS - not
equal to 2) produced by VarScan2.

It includes some duplicated code from FreeBayes, which could be moved to
vcfutils.
use toolz to check for dbsnp key
update SnpEff value for yeast
Merge remote-tracking branch 'upstream/master' into varscan-reject-vcf
Move move_vcf to vcfutils to reduce code duplication
Port to the new location of move_vcf
Add a couple of FIXMEs / TODOs
Merge remote-tracking branch 'upstream/master' into varscan-reject-vcf
Add missing shutil
Use the bgzipped file name for adding the filter

Previous code used the original return value from combine_variants, and
thus the file was without the right extension, causing file_exists() in
the reject calling function to close early, preventing any REJECT records
to be written
shutils -> shutil. Thanks to Piet Jones.
disable vqsr for non-human
Merge pull request #464 from kern3020/master

Modifications to enable non-human run
Small cleanups for #464: add missing parenthesis, whitespace fixes, and simplify dictionary retrieval
Ensure cn.mops samples are correctly extracted when R make.names converts characters. Fixes #462
Document setting user process limit for dealing with open file handle issues: #457
Add link to Luca's poster on using bcbio for ovarian cancer sequencing
Add link to Luca's poster on using bcbio for ovarian cancer sequencing
Improve memory utilization with joint calling by assigning less to main process. Write inputs to list file to make debugging of large runs easier
Handle input metadata with empty information. Fixes #469. Fix typo in hg19 ensembl name. Fixes #467
Update scalpel.py

for ``min_cov`` consistently ``3``