Output from Analyze QIAseq Hybrid Capture DNA
The following outputs are generated:
- Genome browser view (
): Collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. Note that not all output tracks are necessarily in the browser. Tracks can be added and removed from the browser.
- Sample report (
): Sample report containing essential information from all reports produced by the workflow.
- Variants (
): Detected variants.
- Additionally, if 'Analysis options' in the Specify workflow path wizard step is set to create a CNV control:
- Coverage table (
): Coverage for every target region position. Can be used as control in Copy Number Variant Detection (Targeted).
- Coverage table (
- Additionally, if detecting CNVs:
- Gene-level CNV track (
): Genes affected by CNVs.
- Gene-level CNV track (
- Additionally, if mitochondrial analysis is included:
- Variants mito (): Variants detected in mitochondrial spike-in target regions.
- Variants mito (
- Additionally, if preparing for QCI Interpret:
- QCI Interpret report (): Report prepared for uploading to QCI Interpret and QCI Interpret Translational.
- QCI Interpret report (
- QC & Reports folder:
- Coverage report (
): Summarizes coverage statistics in target regions.
- Duplicates report (
): Contains information about removal of duplicate mapped reads
- Mapping report (): Summarizes the performed read mapping.
- QC report (): Summarizes and visualizes various statistics of the input reads.
- Structural variants report (): Summarizes the number and different types of identified structural variants.
- Trim reads report (): Summarizes the performed read trimming
- Additionally, if mitochondrial analysis is included:
- Coverage report mito (): Summarizes coverage statistics in mitochondrial spike-in target regions.
- Coverage report mito (
- Additionally, if detecting CNVs:
- CNV results report (): Summarizes the identified CNVs.
- CNV results report (
- Coverage report (
- Tracks folder:
- Amino acid changes (
): Amino acid changes introduced by the detected variants.
- Indels indirect evidence (): Filtered indels.
- Per-region statistics track (): Coverage statistics for each target region.
- Read mapping (
): Reads mapped to the reference genome.
- Additionally, if mitochondrial analysis is included:
- Amino acid changes mito (): Amino acid changes introduced by the detected variants in mitochondrial spike-in target regions.
- Indels indirect evidence mito (): Indels in mitochondrial spike-in target regions.
- Per-region statistics track mito (): Coverage statistics for each mitochondrial spike-in target region.
- Amino acid changes mito (
- Additionally, if detecting CNVs:
- Region-level CNV track (): Regions affected by CNVs.
- Target-level CNV track (): Targets used for CNV detection.
- Region-level CNV track (
- Amino acid changes (