Try out GTGT via the website of the Dutch Center for RNA Therapeutics: https://gtgt.rnatherapy.nl.
The documentation is available on http://gtgt.readthedocs.io/.
To speed up the tool, you can enable caching by setting the GTGT_CACHE environment variable.
gtgt transcript ENST00000241453.12 | jq .
gtgt links "NM_000094.4:c.5299G>C"
Use the analyze entry point to generate all exon skips, and compare them to the wildtype and patient transcripts
# A frameshift deletion in exon 2
$ gtgt analyze ENST00000375549.8:c.100del
{
"wildtype": 1.0,
"ENST00000375549.8:c.50_172del": 0.8048779330148124,
"patient": 0.3513663563397666,
"ENST00000375549.8:c.167_317del": 0.3513663563397666
}
# An in-frame deletion in exon 2, notice how non of the exon skips have a
# higher score than the patient
$ gtgt analyze ENST00000375549.8:c.100_102del
{
"wildtype": 1.0,
"patient": 0.9970458173607387,
"ENST00000375549.8:c.50_172del": 0.8048779330148124,
"ENST00000375549.8:c.167_317del": 0.3484121737005053
}
# An in-frame deletion that creates a STOP codon is recognized as
# as highly detrimental
$ gtgt analyze ENST00000452863.10:c.87_89del
{
"wildtype": 1.0,
"patient": 0.18847136926335686,
"ENST00000452863.10:c.659_787del": 0.18847136926335686,
"ENST00000452863.10:c.782_890del": 0.18847136926335686,
"ENST00000452863.10:c.885_968del": 0.18847136926335686,
"ENST00000452863.10:c.963_1019del": 0.18847136926335686,
"ENST00000452863.10:c.1014_1116del": 0.18847136926335686,
"ENST00000452863.10:c.1111_1267del": 0.18847136926335686,
"ENST00000452863.10:c.1262_1357del": 0.18847136926335686,
"ENST00000452863.10:c.1352_1450del": 0.18847136926335686
}
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