etal cnvkit issues - Githubissues

etal / cnvkit

Copy number variant detection from targeted DNA sequencing

http://cnvkit.readthedocs.org

Other

502 stars 162 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Getting BAF and allelic imbalance in export vcf

#892 GACGAMA opened 4 days ago
0
Unable to produce .cnr files

#891 nithishak opened 6 days ago
2
Installation error

#890 mikewojnowicz opened 1 week ago
0
No Results

#889 rmormando opened 1 week ago
1
build(deps): bump scikit-learn from 1.2.1 to 1.5.0 in /requirements

#888 dependabot[bot] opened 1 week ago
0
how to install the cnvkit v0.9.11 by the tar.gz source

#887 litun-fkby opened 2 weeks ago
0
Running CNVkit with VCF files

#886 GACGAMA opened 2 weeks ago
0
How to merge vcfs of different samples?

#885 zyxNo1 opened 3 weeks ago
0
baits and target bed file

#884 bagieutopia opened 3 weeks ago
0
The problem of false negative in male sex chromosomes

#883 zhuying412 opened 1 month ago
0
Using CNVkit with THetA2 and "Sample_paired.vcf"?

#882 ngs-seqer opened 1 month ago
0
subprocess.CalledProcessError when segmenting

#881 sainsachiko opened 1 month ago
3
Update conda recipe with build.run_exports version pin (#877)

#880 etal opened 2 months ago
0
Command fixes

#879 etal closed 2 months ago
0
Fix deprecation-related errors and warnings

#878 etal closed 2 months ago
0
Next release?

#877 gabeng opened 2 months ago
10
CNVkit batch issue

#876 NIBIL401 closed 2 months ago
2
dockerhub link is dead (typo)

#875 nickhsmith closed 2 months ago
1
Why are the log2 values of the chrX in the female reference I constructed mostly around 1?

#874 zhuying412 opened 3 months ago
0
Fix typos

#873 mr-c closed 3 months ago
1
Issue in running cnvkit.py diagram command

#872 korol996 closed 2 months ago
2
Use correct PAR1/2 start positions.

#870 rollf closed 3 months ago
1
Allow using reference fasta with reference cnn in cnvkit batch when processing crams

#869 IvantheDugtrio opened 4 months ago
1
Runtime Error Using CNVKit Batch

#868 hkarakurt8742 opened 4 months ago
1
cnvkit.py batch hangs on very large WGS dataset

#867 gtollefson opened 4 months ago
0
pysam.idxstats

#866 raygozag opened 5 months ago
0
Need Help with generating Gene level Copy Number Ratio

#865 MaxSimonNm opened 5 months ago
1
Best practices for creating a WGS pooled reference

#864 IvantheDugtrio opened 5 months ago
0
sex allocation incorrect for males; antitarget used over target

#863 alexander-e-f-smith opened 6 months ago
0
TypeError: batch_run_sample() takes from 16 to 17 positional arguments but 18 were given

#862 nash5202 closed 2 months ago
1
Allow manual tuning of smoothing window fraction

#860 kkchau closed 6 months ago
1
Smoothing window fraction fix results in noisier data in targeted sequencing panel?

#859 kkchau opened 7 months ago
1
Adding gene diagram to heat map

#858 evcon131 opened 7 months ago
0
what are the steps for Germline and Somatic CNV detection using CNVkit?

#857 ahmadsam66 opened 7 months ago
0
What format is the input bam file?

#856 luckilyG opened 8 months ago
0
What's the mean of CN column？

#855 yuanpingdu opened 8 months ago
0
cnvkit.py export bed

#854 lmanchon opened 8 months ago
0
cnvkit for multiple wgs cohort

#853 zhaowsong closed 6 months ago
0
question about the segment threshold

#852 litun-fkby opened 8 months ago
0
Fix sample gender input #843

#851 28rietd closed 7 months ago
1
TypeError and AttributeError when running 'cnvkit.py target baits.bed --annotate refFlat.txt --split -o targets.bed'

#850 Lei-Guo opened 9 months ago
0
Can I use cnvkit software to evaluate the copy number of genes ？

#849 zhoudreames opened 9 months ago
0
Error Installing CNVKit via Miniconda

#848 James-Brundage closed 9 months ago
1
CNVkit for RNA-seq: log2 in *.cnr file is all zero

#847 jingyu9603 opened 9 months ago
0
sex inference and X chromosome copy number

#846 albamasmalavila opened 9 months ago
0
Why adding a pseudocount of flat reference to the aggregated reference?

#845 28rietd opened 9 months ago
0
Update minor version of pomegranate

#844 kkchau closed 9 months ago
1
We could not set the gender of the sample correctly in reference.py

#843 ccoo22 closed 7 months ago
2
build(deps): bump reportlab from 3.6.8 to 3.6.13 in /requirements

#842 dependabot[bot] closed 9 months ago
0
Docker image of cnvkit does not contain additional scripts

#841 MatteoSchiavinato closed 2 months ago
3