CLI plotly sashimi

  
  usage: sashimi.py [-h] -c COORDINATES -b BAM -g GTF [-o OUTPUT] [-s STRAND] [-v VCF] [-sa SPLICEAI] [-gb {grch37,grch38}] [-t TEMP]
                    [-r REFERENCE]
  
  Browsable html sashimi
  
  options:
    -h, --help            show this help message and exit
    -c COORDINATES, --coordinates COORDINATES as: "chr:start-end"
    -b BAM, --bam BAM file
    -g GTF, --gtf GTF file
    -o OUTPUT, --output OUTPUT
    -s STRAND, --strand STRAND {default= unstranded}
    -v VCF, --vcf VCF
    -sa SPLICEAI, --spliceai SPLICEAI {False, True}
    -gb {grch37,grch38}, --genomebuild {grch37, grch38} // needed for SpliceAI
    -t TEMP, --temp TEMP // temp folder needed to store subset of vcf and SpliceAI annotated vcf.
    -r REFERENCE, --reference REFERENCE // genome fasta, see 'spliceai' python package for download instructions.