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

• Generating brass filter file -filter|f
• Regions of excessive depth -depth|d
• Genome Cache File -g_cache|gc
• Viral Sequences -viral|vi
• Microbial Sequences -microbe|mi
• Centromere Telomere locations -centtel|ct
• Generate GC bins -gcbins|b
• Getting cytoband file -cytoband|cb

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

• BEDPE
• BEDPE - Fusion flag
• Intermediates and Filtering

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