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etal
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cnvkit
Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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How to export segments
#739
gtollefson
opened
2 years ago
1
Hard coded additional GC content filter in fix.py module
#738
tsivaarumugam
closed
1 year ago
3
Why do I get a extra targets.bed?
#737
idoit4fun
closed
2 years ago
2
Make clear in the documentation that the batch command is also running "call"
#736
LukaP-BB
opened
2 years ago
4
How to get the ensembl-gene-info.hg19.tsv file for RNAseq CNV?
#735
xiucz
opened
2 years ago
0
Query regarding identifying gene level CNVs, autobin and bintest
#734
LavanyaRanganathan95
opened
2 years ago
1
Combining reference
#733
harish0201
opened
2 years ago
1
How is generated the heatmap?
#732
msubirana
closed
1 year ago
2
Why the bins failed filters?
#707
HEKntg
opened
2 years ago
0
AssertionError import-rna
#706
Argonvi
opened
2 years ago
2
How to build a .cnn file without normal bam?
#705
lwlive
opened
2 years ago
0
I couldn't understand how to caculate log2 ratio for bins just reading the CNVkit documentation ,who knows can reply me ?
#704
whiffen-cann
opened
2 years ago
2
call, segmetrics: Filter by Bayesian mixture model
#703
etal
opened
2 years ago
0
what is the principle of copy number calculating between tumor and WT?
#702
jlchen5
opened
2 years ago
0
Is there any good ideas about which options/method of cnvkit would be recommended when calling CNAs in ctDNA samples? Due to unknown sample purity ,I hava got so much genes and segments in my ctDNA sample with subcommand genemetrics.
#701
whiffen-cann
opened
2 years ago
2
Unexpectedly high log2 ratios for some but not all samples
#700
zetamui
opened
2 years ago
2
Makefile portabilty for CNVkit self-tests (661)
#699
tetedange13
closed
2 years ago
0
How to get raw vcf without filtering CNV events?
#698
xiucz
opened
2 years ago
2
what's the meaning of p_ttest in call.cns file ?I cannot find any description about this value .
#697
whiffen-cann
opened
2 years ago
2
CNVkit batch command cannot recognise bed file format
#696
HasibAhmed1996
closed
2 years ago
4
Makefile portability: use variables for Rscript and Python, and set --rscript-path explicitly
#695
etal
opened
2 years ago
2
segmetrics: apply --drop-low-coverage option as skip_low in the API
#694
etal
closed
2 years ago
1
bintest: set 'probes' column to 1 in output
#693
etal
closed
2 years ago
0
Value Error: Duplicated genomic coordinates in sample set due to different transcripts
#692
ktr0nimus
closed
2 years ago
2
What is the default target-avg-size for wgs?
#691
ytakemon
closed
2 years ago
2
Segmentation result dubious?
#690
marchoeppner
opened
2 years ago
3
BAM after MarkDuplicates with Picard produces different CNV calling results with BAM that has the duplicates *removed* with Picard
#689
zetamui
opened
2 years ago
2
Gene name missing from annotations in calls file
#688
micknudsen
opened
2 years ago
3
batch command parameter usage
#687
enes-ak
opened
2 years ago
1
Installing via pip on CentOS and finding atlas libraries
#684
astrophys
closed
1 year ago
3
No coverage on CDKN2A gene caused false-negative CN segment
#683
zhuhenan
opened
2 years ago
2
Plot copy number integer with segment
#682
jnaccara
opened
2 years ago
2
what is resolution in cnv?
#681
jeongmeani
opened
2 years ago
1
IO test fails on nosample.vcf file
#680
jbedo
opened
2 years ago
2
cnvkit access fails to add >NC* named regions to the .bed file
#679
vmukhina
opened
2 years ago
1
pysam.utils.SamtoolsError: "samtools returned with error 2
#678
philtat
closed
2 years ago
3
Start and end coordinates switched - is this expected?
#677
kkchau
opened
2 years ago
4
Can i use tumor samples to generate reference files?
#676
weizhiting
closed
2 years ago
3
weird results
#675
xinmiaoyan
opened
2 years ago
1
how long will cnvkit run a case?
#674
xinmiaoyan
closed
2 years ago
0
Germ-line exomes, single samples
#673
marchoeppner
opened
2 years ago
0
a same command fails in the first time
#672
asmlgkj
opened
2 years ago
2
export VCF
#671
SouzaBB
opened
2 years ago
2
CNVkit failed on CNVs simulation
#670
lmanchon
opened
2 years ago
2
custom genome and sex chromosome error
#669
acontrerasg
opened
2 years ago
2
ValueError: Reference is missing 1 bins found in xx.sort_dedup
#668
asmlgkj
closed
2 years ago
3
Use of cnvkit in germline haploid samples
#667
pabloangulo7
opened
2 years ago
0
make: python: Command not found make: *** [Makefile:50: build/reference-picard.cnn] Error 127
#666
TheMuffinMan563
closed
2 years ago
2
CNV size
#665
lmanchon
opened
2 years ago
0
Display numerical range and color scale in plots in diagram/ideogram and heatmap
#664
Optimistix
opened
2 years ago
3
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