Skip to content
Keiran Raine edited this page Jan 28, 2022 · 19 revisions

This area contains various guides to help you set up reference files for the overall processing script brass.pl.

BRASS is only suitable for Whole genome sequencing experiments.

Primary outputs

File Description
*.mt.brass.brm.bam Mutant sample aberrantly paired reads excluding high depth regions and skipped contigs
*.wt.brass.brm.bam Wildtype sample aberrantly paired reads excluding high depth regions and skipped contigs
*.brass.annot.bedpe.gz Final output in bedpe format
*.brass.annot.vcf.gz Final output in vcf format
*.brass.ngscn.abs_cn.bw BigWig absolute copynumber
*.brass.intermediates.tar.gz Intermediate files

Reference with: Landscape of somatic mutations in 560 breast cancer whole genome sequences. Nik-Zainal S, et al.

Clone this wiki locally