RNA
|
System Name / Output Folder Names |
File Output Type |
Content |
Software Component |
|---|---|---|---|
|
{Sample_ID} |
*_HighConfidenceVariants.csv |
High confidence fusion and splice variants for each sample. |
Not applicable |
|
Other_Outputs/ RNA_IntermediateFiles/ Alignment |
*.bam *.bam.bai |
Aligned BAM and BAI files from BWA for each sample. |
STAR SAMTools SuperDuper |
|
Other_Outputs/
|
*_Fusions.csv *_FusionFilter.csv |
Fusion and filtered fusion CSV files for each sample. Raw and combined fusion candidates. |
Manta RNAFusionFilter |
|
Other_Outputs/
|
*_SpliceVariants.vcf *.tsv *_fusions.tsv |
Splice variant VCF and TSV for each sample. |
Splice Variant Caller |
|
Other_Outputs/ RNA_IntermediateFiles/ Annotation |
*_SpliceVariants.json |
Annotated splice variants for each sample. |
Illumina Annotation Engine |