Add option to only include PASS SVs when building DB

J35P312 / SVDB

structural variant database software

MIT License

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Add option to only include PASS SVs when building DB #24

Closed fgvieira closed 5 years ago

fgvieira commented 5 years ago

Hi,

would it be possible to have an option to only include SVs (e.g.) with FILTER=PASS when building the DB? Right now svdb --build uses all SVs, but sometimes it would be nice to have the option to only include the ones that PASS. thanks,

J35P312 commented 5 years ago

Hello! Sorry for the delay! I have now added such option:

svdb --build --folder /home/jesper/P1426/Delly/ --prefix DellyPASS --passonly

However, it adds variants with FILTER=Pass or FILTER=. (I have noticed that some callers do not set the filter for low quality calls); Feel free to try!