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Published 20 hours ago • verified publisher icon imgag

LongReads: Implement CNV calling

Open leonschuetz opened this issue 1 year ago • 3 comments

Snakemake code: https://github.com/imgag/megLR/blob/main/workflow/rules/cnv.smk

  • [x] implement

leonschuetz avatar Feb 16 '23 09:02 leonschuetz

switched to ClinCNV since cnvkit results were not sufficient and implementation is difficult

leonschuetz avatar May 08 '23 10:05 leonschuetz

  • implemented with 10000 bin size

  • [ ] adjust filter in GSvar (many false positives)

  • [ ] validate with positive cointrols

leonschuetz avatar Jul 12 '23 11:07 leonschuetz

  • [x] come up with a solution for the pipeline test for CNVs

leonschuetz avatar Jul 21 '23 09:07 leonschuetz