« Changelog History


bcbio-nextgen v0.7.3 Release Notes

Release Date: 2013-09-22 // over 10 years ago
    • 🚚 Move specification of supporting genome files for variation (dbSNP, training files) and RNA-seq (transcript GTF files) analyses into an organism specific resources file. Improves ability to support additional organisms and genome builds.
    • Provide paired tumor/normal variant calling with VarScan. Thanks to Luca Beltrame.
    • Require bash shell and use of pipefail for piped commands. Ensures rapid detection of failures during piped steps like alignment.
    • 🔀 Use samtools cat for post-BAM merging to avoid issues with bamtools requirement for open file handles.
    • ➕ Add installation/upgrade options to enable commercially restricted and data intensive third party tools.
    • 👌 Support for GATK 2.7
    • 🛠 Fixes for TopHat 2.0.9 support: remove extra non-mate match paired end reads from alignment output.
    • Pull description sample names from BAM files if not present in input configuration file. Thanks to Paul Tang for suggestion.
    • 🐛 Bug fixes for non-paired RNA-seq analysis.
    • ➕ Add custom filtration of FreeBayes samples using bcbio.variation.
    • 0️⃣ Default to phred33 format for Tophat alignment if none specified.