We deliver data in different ways for different types of applications.
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
Contact us for discussion about access to this service.
We deliver raw data from sequencing (FASTQ files). Deliveries are done to our
For microbial samples a QC analysis report is delivered together with the raw data
We also have a typing pipeline microSALT that determines a sample's organism specific
sequencing type and it's resistance pattern.
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).
|QC-values from the analysis (duplication rate, on-target, coverage, etc.)|
|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) callers|
|VEP annotated VCF file with merged, filtered and passed somatic SVs, CNVs and InDels|
|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|
|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)|
|Raw VCF with somatic and small InDels and SNVs|
|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|
|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.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.