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NAME

AnnotateVcf.pl - Annotate variants - Sub/Snp, Insertion, Deletion, ComplexInDel

SYNOPSIS

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)

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