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Parsoa / Nebula

Ultra-efficient mapping-free structural variation genotyper
https://doi.org/10.1093/nar/gkab025
MIT License
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Reducing memory consumption #6

Open cassisnaro opened 3 years ago

cassisnaro commented 3 years ago

Hi, I am trying to run the preprocessing step of nebula on a BAM with long reads, in order to later on call it on short read BAMs. However, I am running out of memory: with the entire BED file, 450GB of RAM was not enough. If I take only a fraction of the BED it works, but I am not sure how to then do the merge. Will Nebula consider it as multiple samples? Thanks

Parsoa commented 3 years ago

Hi,

Nebula is not meant to be used and has not been tested with long read (PB or ONT) BAM files with high-error rates. This may result in excessive amounts of kmers being extracted.