Table of contents
Data delivery
There are several data delivery options available: Scout delivery, Raw data delivery, Microbial analysis delivery and Cancer analysis delivery. The application decides what data delivery option that is possible to select. Not all options are available for all applications, see more info below.
Scout delivery
Scout is our visualisation tool for annotated and ranked variants. The analysis is applicable to whole genomes, exomes and panel samples.
The data is first analysed using one of our pipelines; MIP or BALSAMIC.
- MIP (Mutation Identification Pipeline) is developed by CMMS (Karolinska Institutet) focusing on diagnosis of monogenic, hereditary diseases. Read more in the official documentation for MIP. The standard delivery of the results from sequencing and MIP analysis, is through Scout, which is an application accredited by SWEDAC.
- BALSAMIC (Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer), read more in the section “Cancer analysis delivery” below.
To be able to access Scout, you need to be a registered user. Contact us for more information.
Raw data delivery
For all applications, delivery of raw data files from sequencing (FASTQ files) is possible. This delivery goes through our delivery server.
Microbial analysis delivery
For microbial samples, the delivery consists of a QC analysis report and raw data files (FASTQ files).
The data can also be analysed using our typing pipeline microSALT, determining a sample's organism specific sequencing type and its resistance pattern. This is an analysis accredited by SWEDAC. Read more in the official documentation for microSALT.
Cancer analysis delivery
Our cancer analysis pipeline is called BALSAMIC (Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer) and is analysing both tumor-normal (TN) pairs and tumor only (TO) samples. Read more in the official documentation for BALSAMIC.
BALSAMIC analysis with the myeloid panel (GMSmyeloid) is an application accredited by SWEDAC. Read the summary of the validation and the limitations of the assay here.
From our somatic workflow we deliver the following files depending on the requested analysis: Target Genome Analysis (TGA; including Whole Exome Sequencing) or Whole Genome Sequencing (WGS).
Common TGA and WGS delivered files
| File | Order type | Description |
|---|---|---|
| multiqc_report.htmlTO,TN | balsamic/Scout balsamic_umi/Scout balsamic_qc | QC-values from the analysis (duplication rate, on-target, coverage, etc.) |
| delivery_report.htmlTO,TN | balsamic/Scout balsamic_umi/Scout balsamic_qc | Delivery report showing sequencing and bioinformatic analysis characteristics and metrics |
| tumor.merged.cramTO,TN | balsamic/Scout balsamic_umi balsamic_qc | Tumor sample sequencing alignment data (compressed version of a BAM file) |
| normal.merged.cramTN | balsamic/Scout balsamic_umi balsamic_qc | Normal sample sequencing alignment data (compressed version of a BAM file) |
| svdb.vcf.gzTO,TN | balsamic balsamic_umi | Raw VCF containing the merged output of SV (Manta, Delly) and CNV (CNVkit, AscatNgs, Delly, CNVpytor) callers |
| svdb.research.filtered.pass.vcf.gzTO,TN | balsamic balsamic_umi | Research annotated VCF with merged, filtered and passed somatic SVs, CNVs and InDels |
| svdb.clinical.filtered.pass.vcf.gzTO,TN | balsamic/Scout balsamic_umi/Scout | Clinical annotated VCF with merged, filtered and passed somatic SVs, CNVs and InDels |
| dellycnv.cov.gzTO,TN | balsamic | Delly coverage and copy-number profile |
| tumor.dnascope.vcf.gzTO,TN | balsamic balsamic_umi | DNAscope annotated VCF of germline variants in a tumor sample |
| normal.dnascope.vcf.gzTN | balsamic balsamic_umi | DNAscope annotated VCF of germline variants in a normal sample |
| tumor.manta_germline.vcf.gzTO,TN | balsamic balsamic_umi | Manta annotation of germline variants in a tumor sample |
| normal.manta_germline.vcf.gzTN | balsamic balsamic_umi | Manta annotation of germline variants in a normal sample |
| VCF: Variant Calling Format, which is the variant calling output |
TGA specific delivered files
| File | Order type | Description |
|---|---|---|
| tumor_umi_consensusfiltered.merged.cramTO,TN | balsamic_umi/Scout | Tumor sample UMI sequencing alignment data (compressed version of a BAM file) |
| normal_umi_consensusfiltered.merged.cramTN | balsamic_umi/Scout | Normal sample UMI sequencing alignment data (compressed version of a BAM file) |
| vardict.vcf.gzTO,TN | balsamic balsamic_umi | Raw VCF with somatic and small InDels and SNVs |
| vardict.research.filtered.pass.vcf.gzTO,TN | balsamic balsamic_umi | Research annotated VCF file with filtered and passed somatic SNVs and small InDels |
| vardict.clinical.filtered.pass.vcf.gzTO,TN | balsamic/Scout balsamic_umi | Clinical annotated VCF file with filtered and passed somatic SNVs and small InDels |
| tnscope_umi.vcf.gzTO,TN | balsamic_umi | Sentieon TNscope UMI consensus calling raw VCF |
| tnscope_umi.research.filtered.pass.vcf.gzTO,TN | balsamic_umi | Research annotated VCF file with filtered and passed somatic SNPs and InDels |
| tnscope_umi.clinical.filtered.pass.vcf.gzTO,TN | balsamic_umi/Scout | Clinical annotated VCF file with filtered and passed somatic SNPs and InDels |
| tumor.merged.cnsTO,TN | balsamic balsamic_umi | CNVkit segmentation file |
| tumor.merged-diagram.pdfTO,TN | balsamic balsamic_umi | CNVkit diagram of all chromosomes illustrating gain and losses |
| tumor.merged-scatter.pdfTO,TN | balsamic balsamic_umi | CNVkit scatter plot of all chromosomes illustrating gain and losses |
| gene_metricsTO,TN | balsamic balsamic_umi | CNVkit list of genes with copy number gain or loss above or below a threshold |
| cnvkit.vcf2cytosure.cghTO,TN | balsamic/Scout balsamic_umi | CGH format of a CNVkit VCF file |
WGS specific delivered files
| File | Order type | Description |
|---|---|---|
| tnscope.vcf.gzTO,TN | balsamic | Raw VCF output with somatic SNVs, InDels and SVs |
| tnscope.research.filtered.pass.vcf.gzTO,TN | balsamic | Research annotated VCF file with filtered and passed somatic SNVs, InDels and SVs |
| tnscope.clinical.filtered.pass.vcf.gzTO,TN | balsamic | Clinical annotated VCF file with filtered and passed somatic SNVs, InDels and SVs |
| report.pdfTO, TN | balsamic | CNV generated PDF containing plots and sample statistics from AscatTN and CNVpytor |
| ascat.copynumber.txt.gzTN | balsamic | AscatNgs copy number segments data |
| tumor.tiddit_cov.bedTO,TN | balsamic | Coverage profile from TIDDIT of a tumor sample |
| normal.tiddit_cov.bedTN | balsamic | Coverage profile from TIDDIT of a normal sample |
| tumor.vcf2cytosure.cghTO,TN | balsamic | CGH file from TIDDIT coverage and CNVs from a VCF for tumor sample |
| normal.vcf2cytosure.cghTN | balsamic | CGH file from TIDDIT coverage and CNVs from a VCF for normal sample |
Gene fusion analysis delivery
For detection of gene fusions, we are using the nf-core/rnafusion pipeline. Read more in the official documentation for nf-core/rnafusion.
Delivered files
| File | Order type | Description | Uploaded to Scout as |
|---|---|---|---|
| delivery_report.html | rnafusion | Delivery report with case information | Delivery Report |
| fusionreport_index.html | rnafusion | FusionReport of combined fusion calls (all fusions prior filtering) | Rnafusion Report Research |
| fusion_data.vcf.gz | rnafusion | All combined fusion calls in vcf format (all fusions prior filtering) | Clinical fusion variants |
| star_for_starfusion.Aligned.sortedByCoord.out.cram | rnafusion | Sequencing alignment data (compressed version of a BAM file) | RNA splicing |
| star_for_starfusion.Aligned.sortedByCoord.out.cram.crai | rnafusion | Index for alignment | N/A |
| ReadsPerGene.out.tab | rnafusion | Raw gene counts | N/A |
| multiqc_report.html | rnafusion | MultiQC report including QC-values from the analysis (duplication rate, mapping percentage, etc.) | Multiqc Rna |
| fusion_inspector_web.html | rnafusion | FusionInspector report containing combined fusion calls passing filters | Rnafusion Inspector Research |
| combined_fusions_arriba_visualisation.pdf | rnafusion | Arriba visualization of combined fusion calls passing filters | Gene Fusion Report Research |
| arriba.fusions.tsv | rnafusion | Gene fusions detected by Arriba fusion caller | N/A |
| fusioncatcher.fusion-genes.txt | rnafusion | Gene fusions detected by FusionCatcher fusion caller | N/A |
| starfusion.fusion_predictions.tsv | rnafusion | Gene fusions detected by StarFusion fusion caller | N/A |
| FusionInspector.fusions.tsv | rnafusion | Combined gene fusion calls passing filters investigated with FusionInspector | N/A |
| fusioncatcher.summary.txt | rnafusion | Summary output of FusionCatcher calls | N/A |
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