Issues

• CRAM support and potential differences between BAM, MarkDuplicates CRAM, and BQSR-recalibrated CRAM

  question
  etal/cnvkit#1105 · Filter by author mi3112 opened on Jun 10, 2026
  1

• call: FDR correction for called segments

  enhancement
  etal/cnvkit#1034 · Filter by author etal opened on Mar 9, 2026 · v0.9.15

• Somatic CNV benchmark suite

  enhancement
  etal/cnvkit#977 · Filter by author etal opened on Jan 27, 2026 · v1.0

• Avoiding centromere-bridging segments

  enhancement
  etal/cnvkit#969 · Filter by author ilykos opened on Aug 29, 2025 · v0.9.15
  2

• Smoothing window fraction fix results in noisier data in targeted sequencing panel?

  etal/cnvkit#859 · Filter by author kkchau opened on Nov 30, 2023 · v0.9.15
  1

• A question about purity assumption in the Docs

  documentation
  etal/cnvkit#840 · Filter by author RysBen opened on Aug 27, 2023 · v0.9.15

• What are the specific steps to run for cnvkit.py batch -m wgs?

  etal/cnvkit#823 · Filter by author yangdingyangding opened on Jun 16, 2023 · v0.9.15

• Cnvkit call and cnvkit genemetrics_differences + scatter plot

  discussion-candidateplots
  etal/cnvkit#819 · Filter by author MartaRusmini opened on May 24, 2023

• diagram bars size

  etal/cnvkit#814 · Filter by author paumarc opened on May 4, 2023 · v0.9.15

• CNV search in exomes

  discussion-candidate
  etal/cnvkit#813 · Filter by author Zenerzul opened on May 4, 2023

• scatter plot

  discussion-candidateplots
  etal/cnvkit#811 · Filter by author lida-R opened on Apr 24, 2023

• difference between batch bams vs individual bam

  discussion-candidate
  etal/cnvkit#810 · Filter by author a00101 opened on Apr 19, 2023

• cnvkit scatter -Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.

  discussion-candidateplotsquestion
  etal/cnvkit#805 · Filter by author EllenMarieS opened on Mar 23, 2023

• how to convert "Log R Ratio" (log2) to CNV integer

  discussion-candidate
  etal/cnvkit#804 · Filter by author lmanchon opened on Mar 23, 2023

• Whole Genome sequencing CNV calling with a flat reference

  discussion-candidate
  etal/cnvkit#803 · Filter by author justin-greenblatt opened on Mar 23, 2023

• Understand CNVkit output

  discussion-candidate
  etal/cnvkit#801 · Filter by author Nour-EddineS opened on Mar 20, 2023

• precision the CN to decimal and annotate the area where the copy occurs

  discussion-candidate
  etal/cnvkit#797 · Filter by author user-tq opened on Mar 3, 2023
  1

• Bias corrections

  discussion-candidate
  etal/cnvkit#774 · Filter by author MicrobioSee opened on Nov 13, 2022

• The interpretation of results

  discussion-candidate
  etal/cnvkit#762 · Filter by author JD12138 opened on Oct 3, 2022

• --access option resulted in different heatmap

  discussion-candidate
  etal/cnvkit#755 · Filter by author 227BaronChen opened on Sep 2, 2022
  1

• Make clear in the documentation that the batch command is also running "call"

  etal/cnvkit#736 · Filter by author LukaP-BB opened on Apr 25, 2022 · v0.9.15
  4

• How to build a .cnn file without normal bam?

  discussion-candidate
  etal/cnvkit#705 · Filter by author lwlive opened on Mar 7, 2022

• call, segmetrics: Filter by Bayesian mixture model

  enhancement
  etal/cnvkit#703 · Filter by author etal opened on Mar 5, 2022 · v1.0

• what is the principle of copy number calculating between tumor and WT?

  discussion-candidate
  etal/cnvkit#702 · Filter by author jlchen5 opened on Mar 2, 2022

• Unexpectedly high log2 ratios for some but not all samples

  discussion-candidate
  etal/cnvkit#700 · Filter by author zetamui opened on Mar 1, 2022
  2