RNA-seq pipeline test default to GRCh37 not hg19.
Use GRCh37 instead of hg19 for the RNA-seq example
Bump pybedtools to latest version to avoid open file handle issues #627
Add extra RNA-seq annotation files to hg19 resources.
Documentation work: Add DREAM synthetic 3 example replacing older cancer sample (#588). Add methylation work to todo list (fixes #618)
Add joint calling documentation and pointer to write up. Fixes #348
Use bgzipped human_ancestor fasta for LOFTEE to support access with new samtools that on longer uses razip. Fixes #468
add help for bcbio_setup_genome.py
Merge pull request #635 from lpantano/upstream

add help for bcbio_setup_genome.py
Default to a reduced number of split regions (200 instead of 2000) to avoid controller memory issues with large sample sizes
Fix typo
Improve documentation of align_split_size. Fixes #636
Do not gzip fastqs for bowtie
Simple script to cleanly calculate timings from bcbio log files
Remove specific extraction of excessive coverage which doesn't provide enough removal of high coverage regions and causes issues on large populations. Thanks to @lpantano
Enable VQSR on exome analyses with 50 or more samples in a batch
Improvements for coverage: add Chanjo database to upload and correctly prepare unique name file in local directory, replacing if BED file updated
Ensure inputs to chanjo are cleaned and sorted, attempting to avoid issues identified by @lbeltrame
Use vt normalization instead of bcftools normalization to attempt to avoid segmentation faults #639
Add Alla's link to repo. Remove .travis.yml