draft: SnpEff Variant Annotation #16
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Implements and connects a 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 main.nf \
--annotate true \
--genome "genome.fasta" \
--gff "genes.gff" \
--vcf "variants.vcf"
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Description
Implements and connects rudimentary SnpEff Variant Annotation functionality
allowing users to specify:
--annotate) for switching from variant calling to the annotation pipeline--genome)--gff)--vcf) to be annotatedThe expected output will be:
*.eff.vcf)*_summary.html)*_genes.txt) for the identified genesExample call:
nextflow run isugifNF/GATK-flow -r feat/snpeff \ --annotate true \ --genome "genome.fasta" \ --gff "genes.gff" \ --vcf "variants.vcf"Checklist