Command line options | --assembly GRCh38 --cache --cache_version 106 --dir_cache /.vep --everything --filter_common --fork 6 --format vcf --input_file HG00138N.haplotypecaller.filtered.vcf.gz --offline --output_file HG00138N.haplotypecaller.filtered_VEP.ann.vcf --per_gene --plugin dbNSFP,consequence=ALL,dbNSFP4.2a_grch38.gz,rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF --plugin LoF --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz --plugin SpliceRegion --species homo_sapiens --stats_file HG00138N.haplotypecaller.filtered_VEP.summary.html --total_length --vcf |