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.

Scout Variants

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
cram rnafusion Sequencing alignment data (compressed version of a BAM file)
arriba.fusions.tsv rnafusion Gene fusions detected by Arriba fusion caller
fusioncatcher.fusion-genes.txt rnafusion Gene fusions detected by FusionCatcher fusion caller
starfusion.fusion_predictions.tsv rnafusion Gene fusions detected by StarFusion fusion caller
FusionInspector.fusions.tsv rnafusion Combined gene fusion calls investigated with FusionInspector
fusion_inspector_web.html rnafusion FusionInspector report containing combined fusion calls
pdf rnafusion Arriba visualization of combined fusion calls
index.html rnafusion FusionReport of combined fusion calls
multiqc_report.html rnafusion MultiQC report including QC-values from the analysis (duplication rate, mapping percentage, etc.)
software_versions.yml rnafusion List of software versions used for analysis

Contact us for more information about access to our different services.