Variant Detection

Variant detection in Whole-Genome Sequencing data:

Whole-Genome Sequencing (WGS) is a process that determines the complete DNA sequence of an organism's genome. This type of sequencing is mainly used in projects aimed at detecting the presence of SNPs, Indels and structural variants in a sample.

The Oxford Genomics Centre's bioinformatics unit use established analysis pipelines to assist the customer in the interpretation of  WGS data. All sequencing data are first aligned using the the alignment tool STAMPY  and variants are called using the variant detection tool Platypus, both of which have been used in the 1000 genomes project.

The following files will be provided as standard with the resequenced genome:

• Primary QC report  - A file of general QC metrics for each sample sequenced.
• Secondary QC report  - A file of QC metrics for the variants called in each sample.
• FASTQ file – A file of unmapped sequenced reads for each sample.
• A BAM file - An alignment report of sequenced read mapping results.
• A VCF file – An annotated report of the variants called for the sample, including base change, coverage at variant position and variant type.

Optional analyses available:

• A more detailed analysis of variants.
• Custom variant analyses as required by the customer.

  Contact us

Variant detection in exome sequencing data:

Exome sequencing is a technique to selectively sequence the coding regions of the genome as an effective alternative to whole genome sequencing. This type of sequencing is most commonly used in projects aimed at detecting variants related to disease-causing protein structural and functional changes.

The Oxford Genomics Centre's  bioinformatics unit use established analysis pipelines to assist the customer in the interpretation of  Exome sequenced data. All sequence  data are first aligned using the the alignment tool STAMPY  and variants are called using the variant detection tool Platypus, both of which have been used in the 1000 genomes project. The following files will be provided with Exome sequenced data:

• Primary QC report  - A file of general QC metrics for each sample sequenced
• Secondary QC report  - A file of QC metrics for the variants called in each sample
• FASTQ file – A file of unmapped sequenced reads for each sample
• A BAM file - An alignment report of sequenced read mapping results
• A VCF file – An annotated report of the variants called for the sample, including base change, coverage at variant position and variant type

Optional analyses available: 

• A more detailed analysis of variants
• Custom variant analyses as required by the customer

  Contact us