Path 04 · 24 Lessons · 2 Modules

Clinical Variants

Rigorous coverage of Human Genome Variation Society (HGVS) nomenclature and the biocommons toolchain, followed by applied clinical workflows for parsing Variant Call Format (VCF) files, variant normalization, and table annotation.

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By the End

Parse, validate, and format sequence variant descriptions using standard HGVS nomenclature
Normalize genomic variants and project coordinates across genomic, transcript, and protein spaces
Construct structured variant annotation tables from multi-sample VCF files

Progress

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Variant Call Format (VCF) RecordGenomic coordinates against GRCh38 (variants.vcf)

#CHROM  POS       ID          REF  ALT  QUAL   FILTER  INFO
chr17   7676154   .           G    A    99.0   PASS    DP=120;AF=0.51
chr17   43093220  rs80357906  C    T    45.2   PASS    DP=88;AF=0.49

HGVS Nomenclature

Parsing, validation, normalization, and coordinate projection of Human Genome Variation Society (HGVS) variant descriptions across genomic, transcript, and protein references.

11 lessons · 11 graded

AssemblyMapper3 HGVS Nomenclature4 Projection: c. to g. to p.3 SeqRepo3 SequenceVariant4 UTA and Data Providers3 HGVS Normalizer4 HGVS Parser4 HGVS Pitfalls4 HGVS Validator4 HGVS Easy4

Applied Workflows

End-to-end computational pipelines for processing genomic data formats, annotating variant tables, and executing reproducible bioinformatics workflows.

13 lessons · 13 graded

Applied - Annotating a Variant Table4 Applied - Differential Expression Volcano Plot4 Applied - Expression Matrices with NumPy4 Applied - FASTA and FASTQ Workflows4 Applied - GFF and Genomic Intervals4 Applied - Genomic File Formats4 Applied - Heatmaps and Clustermaps4 Applied - Multiple Sequence Alignment Analysis4 Applied - Quality Control Plots4 Applied - Reading VCF with pandas4 Applied - Reproducible Environment4 Applied - Sequence Composition Analysis4 Applied - Variant Normalization Pipeline4

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