how to use filter_vep to filter vcf file
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?
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are these VCFs derived from transcripts? why would an intron be missing from a genomic VCF?
yes, they are from RNAseq