List view

import-rna with control sample

help wanted

mystery

question

rna

Status: Open.

#352 In etal/cnvkit;

· laopp opened on May 10, 2018

cnvkit install in Galaxy - no conda env

enhancement

help wanted

Status: Open.

#431 In etal/cnvkit;

· AjitPS opened on Apr 9, 2019

Update included references for hg38

enhancement

help wanted

Status: Open.

#822 In etal/cnvkit;

· marchoeppner opened on Jun 1, 2023

import-rna: Parameterize fraction of samples with gene expression

enhancement

rna

Status: Open.

#448 In etal/cnvkit;

· etal opened on May 27, 2019

batch: Allow overlapping sets of tumor and normal samples as input

enhancement

Status: Open.

#48 In etal/cnvkit;

· tskir opened on Sep 13, 2015

Missing points in VAF plot

enhancement

plots

question

vcf

Status: Open.

#290 In etal/cnvkit;

· micknudsen opened on Dec 7, 2017

batch hybrid: Use autobin for target and antitarget bin sizes

bug

documentation

enhancement

Status: Open.

#302 In etal/cnvkit;

· etal opened on Jan 22, 2018

diagram: -g/--genes option to label only the specified regions

enhancement

plots

Status: Open.

#248 In etal/cnvkit;

· leiendeckerlu opened on Aug 21, 2017

Unable to use fix without antitarget file for WGS samples

enhancement

Status: Open.

#894 In etal/cnvkit;

· GACGAMA opened on Jul 2, 2024

Improve documentation on cnvkit call and the use of VCFs

documentation

enhancement

vcf

Status: Open.

#616 In etal/cnvkit;

· tskir opened on May 9, 2021

Makefile portability: use variables for Rscript and Python, and set --rscript-path explicitly

enhancement

Status: Open.

#695 In etal/cnvkit;

· etal opened on Feb 22, 2022

reference: Weight pooled normal samples by variance in coverages

enhancement

Status: Open.

#126 In etal/cnvkit;

· etal opened on Aug 30, 2016

CNVkit segment command RuntimeError: Subprocess command failed

bug

mystery

Status: Open.

#901 In etal/cnvkit;

· tanbiswas opened on Jul 31, 2024

segment function fails

bug

mystery

Status: Open.

#896 In etal/cnvkit;

· bounlu opened on Jul 15, 2024

Getting BAF and allelic imbalance in export vcf

enhancement

vcf

Status: Open.

#892 In etal/cnvkit;

· GACGAMA opened on Jun 26, 2024

No Results

bug

Status: Open.

#889 In etal/cnvkit;

· rmormando opened on Jun 19, 2024

Runtime Error Using CNVKit Batch

bug

Status: Open.

#868 In etal/cnvkit;

· hkarakurt8742 opened on Feb 12, 2024

Error while indexing BAM files

enhancement

Status: Open.

#817 In etal/cnvkit;

· brettChapman opened on May 22, 2023

TypeError and AttributeError when running 'cnvkit.py target baits.bed --annotate refFlat.txt --split -o targets.bed'

bug

Status: Open.

#850 In etal/cnvkit;

· Lei-Guo opened on Oct 4, 2023

subprocess.CalledProcessError when segmenting

bug

Status: Open.

#881 In etal/cnvkit;

· sainsachiko opened on May 5, 2024

Unable to produce .cnr files

bug

Status: Open.

#891 In etal/cnvkit;

· nithishak opened on Jun 24, 2024

Improper post-processing of segment [bug]

bug

Status: Open.

#893 In etal/cnvkit;

· GACGAMA opened on Jul 1, 2024

targeted DNA seq

bug

Status: Open.

#908 In etal/cnvkit;

· MaryGoAround opened on Aug 28, 2024

Differnece between running batch and each step individually

bug

mystery

question

Status: Open.

#935 In etal/cnvkit;

· shashwatsahay opened on Dec 21, 2024

Strelka VCF missing GT field causes error during "call" command

bug

vcf

Status: Open.

#943 In etal/cnvkit;

· brandon-hastings opened on Jan 29, 2025