variant-nomenclature-comparison

This project uses multipe tools to generates cDNA and protein nomenclature and produces a spreadsheet comparing the values from each.

Versions

• Python 3.14.3
• Nextflow 25.10.4 build 11173
• UTA uta_20241220
• SeqRepo 2024-12-20

Dependencies

• vcf-sort from vcftools

Running the workflow

Running the workflow in Github Codespaces

This repsoitory has a .devcontainer directory that makes it able to be deployed as a GitHub Codespace. When the Codespace is first launched the .devcontainer/setup.sh script will install necessary dependencies including the hg19 fasta and annovar databases.

To run the workflow change to the nextflow directory and launch the worfklow:

nextflow run .

Variant list

The workflow depends on a variant list. Each tool identifies transcripts and nomenclature for the variants. When the variant_source parameter is set to 'tfx' the variant list will be extracted from the variants fround in the output of the Transcript Effects tool.

Running the workflow locally

To run the workflow on your local environment edit the nextflow/nextflow.config file and make the following changes to the mac profile:

• Set the params.fasta parameter to the full path to the hg19 fasta
• Set the params.uta_schema parameter to the schema in your UTA database
• Set the env ANNOVAR_HOME to directory where you installed annovar.

Example command line for launching the workflow specifying the mac profile

nextflow run main.nf -profile mac main \ 
    --variant_source tfx  \
    --variant_source_file /tmp/transcript_effects/out.json \
    --generate_variant_validator_batch true \
    --mutalyzer_nomenclature_file ../data/mutalyzer/mutalyzer_nomenclature.csv \
    --variant_validator_batch_results ../data/variant_validator/variant_validator_result.tsv