Variant-calling
Variant-calling
Comparing genome variation among populations or looking disease genotypes is a complex task. Finding the variants that illustrate these differences is the first step in understanding these population structures or genotype-phenotype relations.
Keywords
Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Global learning objectives
- Performing a variant calling analysis
- Being able to choose an appropriate strategy {Advanced}
- Recognizing the challenges and pitfalls
- Recognizing issues with the data
- Troubleshooting issues with the data {Advanced}
- To visualize alignments and variants using a genome viewer
- Apply filters to your list of variants
- Evaluate the quality of your alignments and your variants
Modules
Preprocessing
- Applying QC software and interpreting the output
- Deciding/performing necessary preprocessing steps
- Understand the standard file formats for representing sequences
Alignment
- Producing alignment
- Selecting the appropriate tool
- Recognizing the challenges and pitfalls
- Interpreting the aligners output
- Understand the standard file formats for representing sequence alignment
Alignment QC
- Applying QC software and interpreting the output
- Deciding/performing necessary filtering steps
Variant calling
- Understand the standard file formats for representing variant data
- Applying local realignment and recalibration to enhance variant calls quality
- Deciding on filters to remove uninformative - such as technical artefacts - variants
- Performing the variant calling significance analysis
Variant calling QC
- Validating the obtained variants
Variant annotation
- Functionally annotating variants
Exploratory analysis
- Being able to visualise alignments
- Identifying confounding effects and taking necessary action
Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Activity log