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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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How to run without high-coverage regions filter #170

Closed ducerer closed 3 years ago

ducerer commented 3 years ago

Hi,

Smoove run with further filter lumpy_filter calls to remove high-coverage regions, but my data just with true SVs on hign-coverage regions(ctDNA samples sequenced with >20,000X coverage), so, to avoid being filtered out, how can I run soomve without lumpy_filter? or how to set parameters to allow high-coverage data?

Best!

brentp commented 3 years ago

new release here allows this: https://github.com/brentp/smoove/releases/tag/v0.2.8

run with, e.g. 

export SMOOVE_MAX_DEPTH=100000
smoove call ...