Provide additional memory for VQSR when running with multiple cores. Thanks to @lpantano
Remove need for pybedtools when retrieving callable regions to use in bcbio_vm
Provide additional memory based on available cores to GATK CombineVariants to prevent slowdowns with large numbers of samples. Thanks to @lpantano
Merge pull request #658 from lpantano/upstream

fix sample_name in csv when there are paired samples
Skip GATK BaseRecalibration if no file of known variants is found.
Add bcbio_setup_genome.py to the tool directory on installation.
Configure STAR to dump out the file that is needed to run RSEM.
Enable multithreaded parallelization for CombineVariants up to the recommended 4 cores. (cc @lpantano)
Provide post-call filtering of VarDict to remove somatic mutations with equivalent frequency in normal calls. Reduces false positives on synthetic 3 datasets in evaluation. Thanks to @mjafin
Fixed recalibration default text.
Pass R libpath to CNVkit to handle installation in non-standard directories. etal/cnvkit#2
Enable passing in GATK and MuTect jars from S3 as global resources. Download locally and link into configuration to use the remote file. Allows running GATK tools with docker containers.
Avoid re-calculating depth metrics when running post variant calling annotation with GATK to provide accurate metrics on high depth samples. Thanks to @mjafin
Initial support for downloading on-demand pre-prepared genomes from s3 on AWS
Mark checkpointed re-runs in parallel dictionary allowing bcbio-vm to skip creating docker containers. High level target function to allow running all of bcbio inside of a container
Improve interaction of template creation command with S3 -- download and organize resources directly linking to S3 for running
Provide a tools_off option to force using bwa aln approach. Thanks to @JiantaoShi
Pre-filter BED files to remove non-increasing regions (same start/end or end less than start)
Document bcbio-vm AWS integration, including setting up and running analyses
import pybedtools only when it's used

it does something on initialization that takes ~2.5s, which makes
bcbio_vm.py noticably slow