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path 04 · 24 lessons · 2 modules

Clinical Variants

HGVS notation and the biocommons toolchain, then applied pipelines: reading VCFs, normalising variants and building annotated tables.

Start pathEnter

By the end you can

Parse and validate HGVS variant descriptions
Normalise variants and convert between c., g. and p. coordinates
Build an annotated variant table from a VCF

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01

HGVS Nomenclature

Parsing, validating, normalising and projecting variants.

11 lessons

AssemblyMapper HGVS Nomenclature Projection c to g to p SeqRepo SequenceVariant UTA and Data Providers hgvs Normalizer hgvs Parser hgvs Pitfalls hgvs Validator hgvs easy

02

Applied Workflows

Pipelines over real genomic file formats.

13 lessons

Applied - Annotating a Variant Table Applied - Differential Expression Volcano Plot Applied - Expression Matrices with NumPy Applied - FASTA and FASTQ Workflows Applied - GFF and Genomic Intervals Applied - Genomic File Formats Applied - Heatmaps and Clustermaps Applied - Multiple Sequence Alignment Analysis Applied - Quality Control Plots Applied - Reading VCF with pandas Applied - Reproducible Environment Applied - Sequence Composition Analysis Applied - Variant Normalization Pipeline