Genotyping and Variant diagnosis
Biotechvana is delighted to offer to its customers data analysis services for calling and annotation of variants in exome/genome/amplicon/transcriptome HTS approaches. Although each study needs to be specified in the context of your experiment design and the species and/or sample in analysis, below we summarize the usual workflow followed by us in these types of studies.
1) Preprocessing of raw data
2) Mapping on reference
- Quality analysis of raw sequence data files (either single or pair-end)
- Preprocessing of reads (either single or pair-end) including demultiplex and removing of low-quality sequences, primers/adapter remnants
and artifacts and (when appropriate) trimming/clipping, of reads.
3) Alignment post-processing
- Fastq mapping on the reference genome
- Determination of coverage and mapping metrics
4) Variant Calling and annotation
- Read duplicate mark and removal
- Indel realignment
- Base quality score recalibration (BQSR)
5) Filtration and priorization
- Calling of SNPs and Indels
- Panel of Normals (PON) for cancer and liquid biopsy approaches
- Calling of structural variations (inversions, insertions, deletions, CNVs, etc).
- Variant metrics
- Annotation of variants
- Data integration
- Filtering of less reliable variant calls (false positives)
- Filtering group-specific variants
- Filtering and prioritization of variants relative to annotations (i.e. genes, diseases, etc)
If you are interested in getting more information about our services for analysis of VariantSeq data, please contact us at biotechvana(at)biotechvana.com and we will be glad to pass you on a quote or organize a personalized meeting with you in order to discuss and evaluate your experiment.