--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,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,loftee_path:/opt/conda/envs/nf-core-vep-106.1/share/ensembl-vep-106.1-0 --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,spliceai_scores.raw.indel.hg38.vcf.gz --plugin SpliceRegion --species homo_sapiens --stats_file HG00138N.haplotypecaller.filtered_VEP.summary.html --total_length --vcf