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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://Clinical-Genomics.github.io/genmod/
MIT License
78 stars 19 forks source link

Scoring an empty VCF #130

Open fellen31 opened 3 months ago

fellen31 commented 3 months ago

Hi,

Sometimes all variants in a VCF might be filtered out before running genmod.

models will run without error, but fields will be missing in the output header

##INFO=<ID=Annotation,Number=.,Type=String,Description="Annotates what feature(s) this variant belongs to.">
##INFO=<ID=GeneticModels,Number=.,Type=String,Description="':'-separated list of genetic models for this variant.">
##INFO=<ID=ModelScore,Number=.,Type=String,Description="PHRED score for genotype models.">
##INFO=<ID=Compounds,Number=.,Type=String,Description="List of compound pairs for this variant.The list is splitted on ',' family id is separated with compoundswith ':'.>

causing score to fail

[2024-07-25 12:58:48,550] WARNING : genmod.score_variants.check_plugins: INFO field ModelScore is not in vcf INFO. This field will not be scored.
[2024-07-25 12:58:48,550] WARNING : genmod.score_variants.check_plugins: INFO field GeneticModels is not in vcf INFO. This field will not be scored.
[2024-07-25 12:58:48,550] ERROR   : genmod.commands.score_variants: All score plugins has to be defined in vcf header
Aborted!

Could a VCF without any variants be allowed to pass through genmod?