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.
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).
Common 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.) |
| delivery_report.htmlTO,TN | balsamic balsamic_umi balsamic_qc | Delivery report showing sequencing and bioinformatic analysis characteristics and metrics |
| 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, 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 balsamic_umi | 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 | 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.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 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 | 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 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 |
Contact us for more information about access to our different services.