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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Increased hardware requirements and run-time for build38 #336

Open MinocheAE opened 4 years ago

MinocheAE commented 4 years ago

Hi

running Lumpy (v 0.2.13) on NA12878 build38 and comparing it to build37, I observed the following:

The run-time increased from 10 minutes to 10 hours, required RAM increased by 8x and the output contained 40% more variants. About the same amount of variants can not be mapped back to build37 using UCSC lift-over.

Is this also what you observed running Lumpy on build38? As suggested I am using exclude.cnvnator_100bp.GRCh38.20170403.bed.

Is there a way to reduce compute-time and RAM usage as it was for build37?

Thanks