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Keiran Raine edited this page Jan 28, 2022
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This area contains various guides to help you set up reference files for the overall processing script brass.pl
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BRASS is only suitable for Whole genome sequencing experiments.
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Generating brass filter file
-filter|f
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Regions of excessive depth
-depth|d
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Genome Cache File
-g_cache|gc
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Viral Sequences
-viral|vi
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Microbial Sequences
-microbe|mi
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Centromere Telomere locations
-centtel|ct
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Generate GC bins
-gcbins|b
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Getting cytoband file
-cytoband|cb
File | Description |
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*.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.