isofox v2.0

Functional:

• expression using driver gene panel to set new ReportedStatus field
• trim 3' adapter sequence from paired reads
• removed unmapped read analysis
• alt splice junction write trascript, exons and a passing file using driver gene panel reportable status
• fusion write common known fusion type, transcript and exon from canonical if found otherwise any other
• panels: restricted gene IDs only used to limit expression output
• panels: TPM norm file - set non-zero median TPM
• report on gene expression based on cohort comparisons and driver gene panel
• write passing alt-SJs if match known exon del-dup
• load and apply excluded regions file (config: excluded_regions) , slice around regions and drop any read with any part including a supp overlapping

Technical:

• writes TSV files instead of CSV
• use TPM norm to adjust low coverage threshold

Config:

• add alt_sj_cohort_file
• add gene_distribution_file
• add driver gene panel
• add excluded regions file