Table of contents


Data delivery

We deliver data in different ways for different types of applications.

Scout analysis

Applicable to both whole genome and exome samples.
After sequencing the data is analysed using MIP or BALSAMIC. MIP is a pipeline developed by
CMMS(Karolinska Institutet) focusing on diagnosis of monogenic, hereditary diseases.

Read more in the official documentation for MIP (analysis pipeline).

The standard delivery of the results from sequencing and MIP analysis is
through uploading of annotated and ranked variants to our visualisation tool
Scout.
Contact us for discussion about access to this service.

Scout Variants

Raw data delivery

We deliver raw data from sequencing (FASTQ files). Deliveries are done to our
delivery server.

Microbial analysis

For microbial samples a QC analysis report is delivered together with the raw data
(FASTQ files).
We also have a typing pipeline microSALT that determines a sample's organism specific
sequencing type and it's resistance pattern.

Cancer analysis

We have an analysis pipeline for somatic mutations in cancer that can analyse both tumor/normal (TN) pairs and tumor only (TO) samples, BALSAMIC.

BALSAMIC analysis with the myeloid panel (GMSmyeloid) is an accredited application from 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), Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS).

Shared TGA and WGS delivered files

File Order type Description
multiqc_report.htmlTO,TN balsamic
balsamic_umi
balsamic_qc
QC-values from the analysis (duplication rate, on-target, coverage, etc.)
tumor.merged.cramTO,TN balsamic
balsamic_umi
balsamic_qc
Tumor sample sequencing alignment data (compressed version of a BAM file)
normal.merged.cramTN balsamic
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) callers
svdb.all.filtered.pass.vcf.gzTO,TN balsamic
balsamic_umi
VEP annotated VCF file with merged, filtered and passed somatic SVs, CNVs and InDels
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 Tumor sample UMI sequencing alignment data (compressed version of a BAM file)
normal_umi_consensusfiltered.merged.cramTN balsamic_umi 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.all.filtered.pass.vcf.gzTO,TN balsamic
balsamic_umi
VEP 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.all.filtered.pass.vcf.gzTO,TN balsamic_umi VEP 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
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.all.filtered.pass.vcf.gzTO,TN balsamic VEP annotated VCF file with filtered and passed somatic SNVs, InDels and SVs
ascat.output.pdfTN balsamic AscatNgs generated PDF containing plots and sample statistics
ascat.copynumber.txt.gzTN balsamic AscatNgs copy number segments data
dellycnv.cov.gzTO,TN balsamic Delly coverage and copy-number profile
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

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