Command line parameters for FAIL5 thresholds

smehringer / SViper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

BSD 3-Clause "New" or "Revised" License

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Command line parameters for FAIL5 thresholds #6

Closed eldariont closed 3 years ago

eldariont commented 5 years ago

Hi,

currently the thresholds for rejecting a polished variant because of its dissimilarity to the original variant (FAIL5) are hardcoded here: https://github.com/smehringer/SViper/blob/master/include/variant.h#L8

Would it be possible to add user parameters for DEV_SIZE and DEV_POS?

Thank you David

smehringer commented 5 years ago

Hey @eldariont,

can you checkout branch feature_deviation_user_parameter and try out the user parameters for deviation size and pos? I don't have time to check if the output is as expected for the same input so maybe you can check.

(Check the advanced help page with -hh)

Best, Svenja

smehringer commented 3 years ago

@eldariont Feel free to reopen this if it is not fixed for you.