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How do BAM preprocessing differences impact segmentation in CNVkit?

question

Status: Open.

#1049 In etal/cnvkit;

· minhyung0621 opened on May 20, 2026

Numerical regression testing

enhancement

Status: Open.

#1039 In etal/cnvkit;

· etal opened on Mar 11, 2026

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Next

call: FDR correction for called segments

enhancement

Status: Open.

#1034 In etal/cnvkit;

· etal opened on Mar 9, 2026

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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

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v1.0

Add Cancer GIAB to benchmark suite

enhancement

Status: Open.

#977 In etal/cnvkit;

· etal opened on Jan 27, 2026

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v1.0

Avoiding centromere-bridging segments

enhancement

Status: Open.

#969 In etal/cnvkit;

· ilykos opened on Aug 29, 2025

cnvkit.py batch with custom pon early exit 0

question

Status: Open.

#916 In etal/cnvkit;

· oronoc1210 opened on Sep 24, 2024

segment with cbs method - threshold

question

Status: Open.

#905 In etal/cnvkit;

· gevro opened on Aug 13, 2024

Unable to use fix without antitarget file for WGS samples

enhancement

Status: Open.

#894 In etal/cnvkit;

· GACGAMA opened on Jul 2, 2024

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Next

Getting BAF and allelic imbalance in export vcf

enhancement

vcf

Status: Open.

#892 In etal/cnvkit;

· GACGAMA opened on Jun 26, 2024

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Next

Running CNVkit with VCF files

vcf

Status: Open.

#886 In etal/cnvkit;

· GACGAMA opened on Jun 10, 2024

Using CNVkit with THetA2 and "Sample_paired.vcf"?

vcf

Status: Open.

#882 In etal/cnvkit;

· ngs-seqer opened on May 13, 2024