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

question

Status: Open.

#1105 In etal/cnvkit;

· mi3112 opened on Jun 10, 2026

call: FDR correction for called segments

enhancement

Status: Open.

#1034 In etal/cnvkit;

· etal opened on Mar 9, 2026

·  

v1.0

Account for overlapping PE reads from short fragments in coverage command

enhancement

Status: Open.

#999 In etal/cnvkit;

· shashwatsahay opened on Feb 16, 2026

·  

v1.0

Add Cancer GIAB to benchmark suite

enhancement

Status: Open.

#977 In etal/cnvkit;

· etal opened on Jan 27, 2026

·  

v1.0

Avoiding centromere-bridging segments

enhancement

Status: Open.

#969 In etal/cnvkit;

· ilykos opened on Aug 29, 2025

Running CNVkit with VCF files

discussion-candidateUsage question; convert to a GitHub DiscussionUsage question; convert to a GitHub Discussion

vcf

Status: Open.

#886 In etal/cnvkit;

· GACGAMA opened on Jun 10, 2024

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

Status: Open.

#859 In etal/cnvkit;

· kkchau opened on Nov 30, 2023

A question about purity assumption in the Docs

documentation

Status: Open.

#840 In etal/cnvkit;

· RysBen opened on Aug 27, 2023

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

Status: Open.

#823 In etal/cnvkit;

· yangdingyangding opened on Jun 16, 2023

Cnvkit call and cnvkit genemetrics_differences + scatter plot

discussion-candidateUsage question; convert to a GitHub DiscussionUsage question; convert to a GitHub Discussion

plots

Status: Open.

#819 In etal/cnvkit;

· MartaRusmini opened on May 24, 2023

diagram bars size

Status: Open.

#814 In etal/cnvkit;

· paumarc opened on May 4, 2023

CNV search in exomes

discussion-candidateUsage question; convert to a GitHub DiscussionUsage question; convert to a GitHub Discussion

Status: Open.

#813 In etal/cnvkit;

· Zenerzul opened on May 4, 2023