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Sub-package Documentation

The validation sub-package is responsible for pulling supporting reads from the bam file and re-calling events based on the evidence in a standard notation.

Types of Output Files

A variety of intermediate output files are given for the user. These can be used to "drill down" further into events and also for developers debugging when adding new features, etc.

expected name/suffix file type/format content
*.raw_evidence.bam bam raw evidence
*.contigs.bam bam aligned contigs
*.evidence.bed bed evidence collection window regions
*.validation-passed.bed bed validated event positions
* text/tabbed failed events
* text/tabbed validated events
*.contigs.fa fasta assembled contigs
*.contigs.blat_out.pslx pslx results from blatting contigs
*.igv.batch IGV batch file igv batch file

Algorithm Overview