how to use filter_vep to filter vcf file

Question

[htchd]

I'm trying to filter vcf files with the following criteria: 1) Variants with alternate allele depth (i.e. supporting reads) > 5
2) Variants that are deletion > 25 BPs which are likely introns confused as deletion

filter_vep \  
  -i test_SVs.vcf.gz \  
  -o test_panel.vcf.gz \  
  --format vcf \  
  --force_overwrite \  
  --only_matched \  
  --filter "(FORMAT/AD[0:1] > 5) and ((VARIANT_TYPE is not deletion) or (VARIANT_TYPE is deletion and LENGTH <= 25))"

is this the correct way to do it?

[Jeremy Leipzig]

are these VCFs derived from transcripts? why would an intron be missing from a genomic VCF?

[htchd]

yes, they are from RNAseq