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