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where <profile> is a geneid profile for the HMM model.

The default program output is in VCL format written to a file "<annotation>_sites.vcf" in the same directory as the provided transcriptome annotation <annotation.gtf>. The output file can be changed by the command line flag -f.

Requirements

Hardware

For time efficiency, the positions of all genetic variants are loaded into the computer's memory (RAM), so it is to be ensured that enough memory is provided to the Java Virtual Machine. As an orientation, the variants from the 1000 Genomes project phase 1 and phase 2 just for chr22 occupy 6.4 Gb of disk and require ~1.5Gb for running splice site scoring.

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