Admin_CacheFileBuilder.pl - Generates the Vagrent reference data set from the supplied GFF£/GTF and Fasta files
Admin_CacheFileBuilder.pl [-h] [-f /path/to/sequence.fa] [-gff /path/to/annotation.gff] [-sp human] [-as GRCh37] [-d homo_sapiens_core_74_37p] [-c /path/to/CCDS2Sequence.version.txt]
Required Options: --output (-o) Output directory --fasta (-f) Fasta file containing Transcript sequences, can be specified multiple times. --features (-gf) GFF3 or GTF file containing genomic annotation --transcripts (-t) Transcript accession file, (simple list, one accession per line) --species (-sp) Species (ie human, mouse) --assembly (-as) Assembly version (ie GRCh37, GRCm38) --data_version (-d) Reference version number (Ensemble example: homo_sapiens_core_74_37p) Other Options: --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 --debug (-debug) This turns on the debug output, useful if you are having issues with a specific Ensembl build
Hey! The above document had some coding errors, which are explained below:
Non-ASCII character seen before =encoding in 'GFF£/GTF'. Assuming UTF-8