Genotyping and Variant diagnosis
Biotechvana offers bioinformatic services for calling and annotation of variants in exome/genome/amplicon/transcriptome NGS aproaches. 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 this type 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 appropiate) 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 Realigment
- 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 of less reliable variant calls (false positives)
- Filtering group-specific variants
- Filtering and prioritization of variants relative to annotations (i.e. genes, diseases etc)