draft: SnpEff Variant Annotation - Githubissues

isugifNF / GATK-flow

Nextflow implementation of the GATK HaplotypeCaller pipeline

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draft: SnpEff Variant Annotation #16

Open j23414 opened 8 months ago

j23414 commented 8 months ago

Description

Implements and connects rudimentary SnpEff Variant Annotation functionality allowing users to specify:

annotate flag (--annotate) for switching from variant calling to the annotation pipeline
reference genome (--genome)
gene feature file (--gff)
variants file (--vcf) to be annotated

The expected output will be:

an annotated VCF file (*.eff.vcf)
a summary file (*_summary.html)
a detailed gene positions file (*_genes.txt) for the identified genes

Example call:

  nextflow run isugifNF/GATK-flow -r feat/snpeff \
    --annotate true \
    --genome "genome.fasta" \
    --gff "genes.gff" \
    --vcf "variants.vcf"

Checklist

[ ] Check minimal dataset

j23414 commented 4 months ago

Are there any blockers here?