[ensembl-dev] VEP v82: Different handling when SVTYPE is defined in VCF INFO field

[Cyriac Kandoth]

Hi,

For the minimalist VCF and VEP command below, using mus_musculus and
GRCm38, the output VCF appears to skip reporting fields like HGVSc,
ALLELE_NUM, and EXON/INTRON positions. This does not happen if I remove
"SVTYPE=DEL" from the input VCF. Am I breaking VCF conventions by
specifying SVTYPE=DEL? Should it only be used for larger structural
variants?

Thanks,
Cyriac

--
*test.vcf contains:*
##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO
11 96283450 . TG T . PASS SVTYPE=DEL

*VEP v82 command with local GRCm38 cache:*
perl variant_effect_predictor.pl --offline --species mus_musculus
--assembly GRCm38 --vcf --input_file test.vcf --output_file test.vep.vcf
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