Improving --gencode_primary and --flag_gencode_primary - Githubissues

Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

https://www.ensembl.org/vep

Apache License 2.0

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Improving --gencode_primary and --flag_gencode_primary #1734

Closed likhitha-surapaneni closed 3 months ago

likhitha-surapaneni commented 3 months ago

Added incompatible flags
Added warnings for unsupported assemblies
Style changes in description of header for GENCODE_PRIMARY field
Consistency with public-plugins/pull/812

Testing

vep -i input.vcf --gencode_primary --refseq   # Error 
vep -i input.vcf --gencode_primary --gencode_basic # Error
vep -i input.vcf --gencode_primary --merged # No error

vep -i input.vcf --gencode_primary --assembly GRCh37 # Warning 
vep -i input.vcf --gencode_primary  --flag_gencode_primary --species mus_musculus --assembly GRCm39 # Warning