[ensembl-dev] Filtering plugins

[Konrad Karczewski]

Hello again,

I've noticed some odd behavior when using the filtering capability of plugins. I ran the RankFilter plugin with at minimum intron_variant's (--plugin RankFilter,intron_variant) and noticed that instead of not printing the consequence it prints a set of blank fields. In the extreme case, I get a line like:

CSQ=|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||

Is this expected behavior or am I missing something: shouldn't these be removed completely?

Full call: perl variant_effect_predictor.pl -i input.vcf.gz -o output.vcf --cache --compress "gunzip -c" --vcf --force_overwrite --offline --fork 4 --fasta ~/.vep/homo_sapiens/75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin LoF --plugin RankFilter,intron_variant

Thanks!
-Konrad

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