Different LoF confidence when adding --fasta option

konradjk / loftee

MIT License

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Different LoF confidence when adding --fasta option #76

Closed koido closed 3 years ago

koido commented 3 years ago

Thank you for providing a very nice tool. I'm using the LOFTEE GRCh38 plugin with the VEP v100 in offline mode.

I found that adding --fasta option in VEP changes several HC pLoF variants into LC pLoF with GC_TO_GT_DONOR flag. Because your README file does not describe the importance of the --fasta option, I want to confirm which is the expected behavior.

I attached my commands and input/output files as examples. examples.tar.gz

Best regards, Masaru

konradjk commented 3 years ago

Hello!

Definitely adding --fasta will make it more accurate as it then has more information about the reference genome in order to make these calls.

Best, -Konrad