bcbio-nextgen v0.7.4 Release Notes

Release Date: 2013-10-20 // over 10 years ago
    • Framework for indexing input reads using parallel bgzip and grabix, to handle distributed alignment. Enables further distribution of alignment step beyond multicore nodes.
    • Rework of ensemble calling approach to generalize to population level ensemble calls. Provide improved defaults for handle 3 caller consolidation.
    • ๐Ÿ‘Œ Support for Mouse (mm10) variant calling and RNA-seq.
    • For recent versions of Gemini (0.6.3+) do not load filtered variants into database, only including passed variants.
    • ๐Ÿ‘Œ Improve specification of resource parameters, using multiple -r flags instead of single semi-colon separated input. Allow specification of pename resource parameter for selecting correct SGE environment when not automatically found.
    • ๐Ÿ‘Œ Support biobambam's bammarkduplicates2 for duplicate removal.
    • ๐ŸŒฒ Clean up logging handling code to be more resilient to interrupt messages.
    • Speed improvements for selecting unanalyzed and unmapped reads to address bottlenecks during BAM prep phase.
    • ๐Ÿ› Bug fix for algorithm options incorrectly expanded to paths on re-runs. Thanks to Brent Pedersen for report.
    • ๐Ÿ›  Fix for Tophat 2.0.9 support: remove reads with empty read names.
    • ๐Ÿ’พ Save installation and upgrade details to enable cleaner upgrades without needing to respecify genomes, tool directory and other options from installation.