etal/cnvkit

Issues

• Heatmap chromosomes in a different natural order [error]

  #920 opened a month ago by jgarces02
  0

• Can I get compy number between white blood cell bam and adjacent normal tissue bam

  #919 opened 2 months ago by shenhaizhongdechanrao
  0

• Installation error

  #890 opened 3 months ago by mikewojnowicz
  9

• heatmap results explaination

  #918 opened 2 months ago by wlyucl
  0

• cnvkit.py batch with custom pon early exit 0

  #916 opened 2 months ago by oronoc1210
  2

• Installation problems

  #898 opened 4 months ago by EfraMP
  6

• What affects the detection of CNVs？

  #917 opened 2 months ago by fjptwenger
  0

• auto gender detection assignment for reference creation problem

  #915 opened 2 months ago by duartemolha
  0

• call with filters cn, ci, sem

  #906 opened 3 months ago by gevro
  2

• Proper read pairs

  #909 opened 2 months ago by gevro
  2

• Filtering single-cell false positive calls

  #907 opened 2 months ago by gevro
  1

• cnvkit.py coverage does not honor -q option

  #913 opened 2 months ago by ishida-md
  5

• CNVkit segment command RuntimeError: Subprocess command failed

  #901 opened 4 months ago by tanbiswas
  4

• `segment` function fails

  #896 opened 4 months ago by bounlu
  3

• targeted DNA seq

  #908 opened 3 months ago by MaryGoAround
  1

• segment with cbs method - threshold

  #905 opened 3 months ago by gevro
  0

• Possible bug in bin sizes

  #904 opened 3 months ago by gevro
  0

• Blank plots

  #903 opened 3 months ago by gevro
  1

• access command: recommended -s (mingap) value

  #902 opened 3 months ago by gevro
  0

• cnvkit.py segment error

  #900 opened 4 months ago by l0ka
  0

• Unable to load BED file with skgenome

  #899 opened 4 months ago by EfraMP
  0

• Somatic CNV calling in case of pre-existing CNVs

  #897 opened 4 months ago by HenriettaHolze
  0

• subprocess.CalledProcessError when segmenting

  #881 opened 7 months ago by sainsachiko
  4

• Merging segments while running pipeline

  #895 opened 4 months ago by NIBIL401
  0

• Unable to use fix without antitarget file for WGS samples

  #894 opened 5 months ago by GACGAMA
  0

• Improper post-processing of segment [bug]

  #893 opened 5 months ago by GACGAMA
  0

• Unable to produce .cnr files

  #891 opened 5 months ago by nithishak
  2

• Getting BAF and allelic imbalance in export vcf

  #892 opened 5 months ago by GACGAMA
  0

• No Results

  #889 opened 5 months ago by rmormando
  1

• how to install the cnvkit v0.9.11 by the tar.gz source

  #887 opened 5 months ago by litun-fkby
  0

• Running CNVkit with VCF files

  #886 opened 5 months ago by GACGAMA
  0

• How to merge vcfs of different samples?

  #885 opened 6 months ago by zyxNo1
  0

• baits and target bed file

  #884 opened 6 months ago by bagieutopia
  0

• The problem of false negative in male sex chromosomes

  #883 opened 6 months ago by zhuying412
  0

• Using CNVkit with THetA2 and "Sample_paired.vcf"?

  #882 opened 6 months ago by ngs-seqer
  0

• Next release?

  #877 opened 7 months ago by gabeng
  10

• TypeError: batch_run_sample() takes from 16 to 17 positional arguments but 18 were given

  #862 opened 7 months ago by nash5202
  1

• Issue in running cnvkit.py diagram command

  #872 opened 7 months ago by korol996
  2

• CNVkit batch issue

  #876 opened 7 months ago by NIBIL401
  2

• Allow using reference fasta with reference cnn in cnvkit batch when processing crams

  #869 opened 9 months ago by IvantheDugtrio
  1

• dockerhub link is dead (typo)

  #875 opened 7 months ago by nickhsmith
  1

• Runtime Error Using CNVKit Batch

  #868 opened 9 months ago by hkarakurt8742
  1

• Why are the log2 values of the chrX in the female reference I constructed mostly around 1?

  #874 opened 8 months ago by zhuying412
  0

• cnvkit.py batch hangs on very large WGS dataset

  #867 opened 9 months ago by gtollefson
  0

• Need Help with generating Gene level Copy Number Ratio

  #865 opened 10 months ago by MaxSimonNm
  1

• pysam.idxstats

  #866 opened 10 months ago by raygozag
  0

• Best practices for creating a WGS pooled reference

  #864 opened 10 months ago by IvantheDugtrio
  0

• sex allocation incorrect for males; antitarget used over target

  #863 opened a year ago by alexander-e-f-smith
  0

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

  #859 opened a year ago by kkchau
  1

• Adding gene diagram to heat map

  #858 opened a year ago by evcon131
  0