DNA
|
System Name / Output Folder Names |
File Output Type |
Content |
Software Component |
|---|---|---|---|
|
{Sample_ID} |
*_SmallVariants.genome.vcf *_Complex.vcf |
Small variant and complex variant genome VCF files for each sample. |
Pisces Psara Pepe |
|
|
*_CopyNumberVariants.vcf |
Copy number variants for each sample |
CRAFT |
|
Other_Outputs/ DNA_IntermediateFiles/ Alignment |
*.bam *.bam.bai |
Aligned BAM and BAI files from BWA for each sample. |
BWA-MEM SAMtools |
|
|
*._realigned.bam *._realigned.bam.bai |
BAM and BAI files from Hygea for each sample. |
Hygea |
|
|
*._Complex.bam *._Complex.bam.bai |
Aligned Complex BAM and BAI files for each sample. |
Complex Variant Caller |
|
Other_Outputs/ DNA_IntermediateFiles/ Annotation |
*_Complex.json *.json |
Annotated complex and small variant JSONs for each sample. |
Illumina Annotation Engine |
|
Other_Outputs/ DNA_IntermediateFiles/ MSI |
*_MSI.json |
Microsatellite results JSON for each sample. |
Hubble |