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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
222 stars 21 forks source link

pre-processing for split & discordant read-pairs? #223

Closed heidihyang closed 11 months ago

heidihyang commented 11 months ago

Hi, I was wondering if I would still need to do the pre-processing require by lumpy? Or if that is part of the workflow of smoove to extract the split and discordant read-pairs? Thanks!

brentp commented 11 months ago

no pre-processing, just run on the bams (aligned by bwa mem).