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