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

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF