AnnotateVcf.pl - Annotate variants - Sub/Snp, Insertion, Deletion, ComplexInDel
AnnotateVcf.pl [-h] [-t] -i <IN_FILE> -o <OUT_FILE> -c <VAGRENT_CACHE_FILE> [-sp <SPECIES> -as <GENOME_VERSON>]
General Options: --help (-h) Brief documentation --input (-i) Input vcf file (expects *.bgz) --output (-o) Output vcf file (plain text, add -t for zip and index) --cache (-c) Vagrent reference data cache file Conditional (can be specified if missing from the input VCF file) --species (-sp) Species --assembly (-as) Genome assembly version Optional --novalid (-n) Don't validate the input/output VCF - Allows unheaded tsv file with VCF column format, cols - 1-6 required, 7-11 as '.' - Does not generate a valid VCF --version (-v) Output version number --process (-p) ID_PROCESS that generated this file --tabix (-t) bgzip and tabix index the output file (will generate the .gz version of the -o option)