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NAME

Admin_EnsemblReferenceFileGenerator.pl - Generates the Vagrent reference files from the specified Ensembl URL

SYNOPSIS

Admin_EnsemblReferenceFileGenerator.pl [-h] [-sp Human] [-as GRCh37] [-d homo_sapiens_core_74_37p] [-f <ftp://ftp.ensembl.org/pub/release-XX/fasta/XXX_XXX/cdna/>] [-o /path/to/output/directory]

  Required Options:

    --output       (-o)     Output directory    

    --species      (-sp)    Species (ie human, mouse)

    --assembly     (-as)    Assembly version (ie GRCh37, GRCm38)

    --database     (-d)     Ensembl core database version number (ie homo_sapiens_core_74_37p)

  Dynamic Download:
  
    --ftp          (-f)     Ensembl ftp directory containing the cDNA fasta sequence files

  Or Local Files:
  
    --features     (-gf)    gff3 or gtf file containing transcript and gene information
  
    --cdna_fa      (-cf)    Fasta file containing protein coding cdna sequences
  
    --ncrna_fa     (-nf)    Fasta file containing non-coding cdna sequences 

  Optional:
  
    --help         (-h)     Brief documentation
        
    --ccds         (-c)     (Recommended) The CCDS2Sequence file from the relevant CCDS release, see http://www.ncbi.nlm.nih.gov/CCDS
    
    --fai          (-fai)   (Recommended) The samtools fasts index file (.fai) for your reference genome
                              This is the reference genome that your bam and vcf files will be mapped to
    
    --trans_list   (-tl)    List of preprepared transcript accessions, only these accesions will be included in the reference output

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