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 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.
To be able to access Scout, you need to be a registered user. Contact us for more information.
For all applications, delivery of raw data files from sequencing (FASTQ files) is possible. This delivery goes through our delivery server.
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.
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).
|QC-values from the analysis (duplication rate, on-target, coverage, etc.)|
|Delivery report showing sequencing and bioinformatic analysis characteristics and metrics|
|Tumor sample sequencing alignment data (compressed version of a BAM file)|
|Normal sample sequencing alignment data (compressed version of a BAM file)|
|Raw VCF containing the merged output of SV (Manta, Delly) and CNV (CNVkit, AscatNgs, Delly, CNVpytor) callers|
|Research annotated VCF with merged, filtered and passed somatic SVs, CNVs and InDels|
|Clinical annotated VCF with merged, filtered and passed somatic SVs, CNVs and InDels|
|dellycnv.cov.gzTO,TN||balsamic||Delly coverage and copy-number profile|
|DNAscope annotated VCF of germline variants in a tumor sample|
|DNAscope annotated VCF of germline variants in a normal sample|
|Manta annotation of germline variants in a tumor sample|
|Manta annotation of germline variants in a normal sample|
|VCF: Variant Calling Format, which is the variant calling output |
|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)|
|Raw VCF with somatic and small InDels and SNVs|
|Research annotated VCF file with filtered and passed somatic SNVs and small InDels|
|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|
|CNVkit segmentation file|
|CNVkit diagram of all chromosomes illustrating gain and losses|
|CNVkit scatter plot of all chromosomes illustrating gain and losses|
|CNVkit list of genes with copy number gain or loss above or below a threshold|
|CGH format of a CNVkit VCF file|
|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|
For detection of gene fusions, we are using the nf-core/rnafusion pipeline. Read more in the official documentation for nf-core/rnafusion.
|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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