WHAT’S NEW

New Tools

  • Muse somatic caller: This tool has been added to the Parabricks toolkit and has a 10x acceleration compared to its original implementation. Muse is the fifth somatic caller in Parabricks. Muse utilizes a novel approach to mutation calling based on the F81 Markov substitution model for molecular evolution, which models the evolution of the reference allele to the allelic composition of the matched tumor and normal tissue at each genomic locus. You can read more here: https://bioinformatics.mdanderson.org/public-software/muse/

Improvement and Bug Fixes

General

  • GenotypeGVCF now support .gz files.

  • TriocombineGVCF and genotypegvcf problem with deepvariant’s gvcfs are fixed.

Germline/Somatic

  • Fix a CRAM support bug for fq2bam.

  • Two sources of deadlock in lofreq are fixed

  • Strelka workflow now accepts interval files

RNA

  • STAR deadlock bug is fixed

  • STAR is around 2 times faster for specific set of data.

  • splitncigar is significantly faster than before

QC

  • Fix a report generation bug for collectmultiplemetrics when specify –gen-alignment –gen-insert-size