Bioinformatics practicals

Genomic variant analysis

Two practicals and a coursework workbench that take you from raw sequencing reads to the meaning of a genetic variant. Everything runs in your web browser – a real command line, a Galaxy-style workflow engine, the IGV genome browser, variant annotation with Ensembl VEP and a 3D protein viewer – with nothing to install.

reads→quality control→alignment→variant calling→annotation→filtering→interpretation→protein structure
Practical

Reads to variants

Does NA12878 carry CYP2C19*2, the allele that makes clopidogrel less effective? Find out from her raw exome reads.

  • The Linux command line; FASTQ, SAM/BAM and VCF files
  • FastQC, BWA-MEM, samtools and bcftools
  • Checking a call in IGV
  • The same pipeline in a Galaxy-style workflow engine – and which approach to use when
Start →
Practical

Variants to meaning

Annotate the same variants and decide which of them matter – for prescribing, and for diagnosing rare disease.

  • Ensembl VEP: consequences, transcripts, HGVS names
  • gnomAD frequencies; SIFT, PolyPhen-2, CADD, SpliceAI
  • Why a “synonymous” variant destroys CYP2C19
  • Filtering funnels, star alleles, and variants in 3D
Start →
Coursework

Coursework workbench

Analyse the exome of a child with a new connective-tissue syndrome: call, filter and annotate her variants, check them in the reads and map the change onto the protein.

  • Real samtools and bcftools on your copy of the data
  • The data stay on your computer – nothing is uploaded
  • Notes you can download for your report
Open →

Before you start

  • Use Chrome, Edge, Firefox or Safari on a laptop or desktop computer; a wide screen helps.
  • Do the practicals in order: the second starts from the variants you make in the first.
  • Your progress and answers are saved in this browser on this computer. Use My answers on each page to download them.
  • The pages need an internet connection for the data, for Ensembl VEP and for the database links.

What is real, what is simulated?

  • Real: samtools, bcftools, bgzip and tabix (compiled to WebAssembly and run in your browser); the IGV genome browser; Ensembl VEP; the protein structures; all the data.
  • Replayed: FastQC, BWA and FreeBayes are too large for a browser, so the terminal replays their real output on exactly these reads.
  • The workflow engine imitates Galaxy and runs the same programs as the terminal.

Data: 1000 Genomes Project (NA12878, SRR098401); UCSC hg19/GRCh37; NCBI RefSeq; Ensembl; gnomAD; RCSB PDB. Software: samtools/bcftools/htslib via biowasm and Aioli, igv.js, NGL Viewer (MIT licences). Adapted from the module's Galaxy, IGV, cytochrome P450, VEP and molecular graphics tutorials (© 2020 Tim Hearn and contributors), shared under the Creative Commons BY-NC-SA 2.0 UK licence.