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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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Smoove for WES #182

Closed alisaadat922 closed 2 years ago

alisaadat922 commented 2 years ago

Hello

I want to use Smoove for whole exome sequencing data. It is mentioned that Smoove could be used for exome data https://github.com/brentp/smoove/issues/89

However, the author of Lumpy has mentioned that Lumpy is not designed for exome data: https://github.com/arq5x/lumpy-sv/issues/225#issuecomment-355760390

Overall, do you recommend using Smoove for exome data? If no, can you recommend other tools?

Thank you for the amazing tools! Ali

brentp commented 2 years ago

Hi, smoove will work on exome data (as will lumpy) but it's probably not the best choice. I don't know what the best tools are for exome but I have found those that rely on a population database of existing samples (to track previously seen variability) will work the best.