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.

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