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NAME

Admin_CacheFileBuilder.pl - Generates the Vagrent reference data set from the supplied GFF£/GTF and Fasta files

SYNOPSIS

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                  

POD ERRORS

Hey! The above document had some coding errors, which are explained below:

Around line 820:

Non-ASCII character seen before =encoding in 'GFF£/GTF'. Assuming UTF-8

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