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cnvkit
Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Consider PAR1/2 on Chr X as autosomal
#789
rollf
closed
1 year ago
12
create reference from affected only and no bait files
#788
kmarianski
opened
1 year ago
1
Incremental reference Generation
#787
justin-greenblatt
opened
1 year ago
1
GISTIC overlapp issue
#786
hanico888
opened
1 year ago
0
Different sex estimated from cnr and cns files
#785
ImNotaGit
opened
1 year ago
0
Optionally consider PAR1/2 as diploid in male samples due to reference genome masking
#784
rollf
closed
11 months ago
3
KeyError: '1 not in /home/renoguch/hg19/hg19.fa.'
#783
raynogu
opened
1 year ago
0
make command failed in /test folder
#782
JiayangZhou
closed
1 year ago
2
batch creates FASTA's bed in working dir not in output-dir
#781
solo7773
opened
1 year ago
0
How to integrate the copy numbers of gene.
#780
THZ34
opened
1 year ago
0
Could not retrieve index file for CRAM files
#779
227BaronChen
opened
1 year ago
0
AttributeError: 'Namespace' object has no attribute 'func'
#778
jlchen5
opened
1 year ago
1
Runtime error while running batch process
#777
HeejunJang
opened
1 year ago
6
Can't convert to gistic marker due to input validation
#776
FriederikeHanssen
closed
10 months ago
4
Setting arbitrary bin size for WGS data
#775
ashenflower
opened
1 year ago
3
Bias corrections
#774
MicrobioSee
opened
1 year ago
0
genemetrics result different between 0.9.8 and 0.9.9
#773
pmtmarine
opened
1 year ago
1
Examining conflicts takes forever installing cnvkit with conda
#772
HeejunJang
opened
1 year ago
3
Remove no-longer needed networkx pinning for Py3.9
#771
DavidCain
closed
1 year ago
1
Remove joblib pinning now that pomegranate fixed
#770
DavidCain
closed
1 year ago
4
Docker needed
#769
kopardev
closed
1 year ago
2
Targets: 3948 (1.4789%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0)
#768
WortJohn
closed
1 year ago
3
genemetrics -m flag
#767
ashbig
opened
1 year ago
1
guess_baits.py into target triggers "TypeError: sequence item 0: expected str instance, numpy.float64 found" error
#766
Quentin-Bayard
opened
1 year ago
0
Rscript runtime Error occurred
#765
HeejunJang
closed
1 year ago
10
Fix 'GC_{MAX,MIN}_FRAC' reference (#763)
#764
tetedange13
closed
1 year ago
1
NameError: name 'GC_MIN_FRACTION' is not defined
#763
HeejunJang
closed
1 year ago
1
The interpretation of results
#762
JD12138
opened
1 year ago
0
CNVKit 0.9.9 Batch mode has inconsistent CN and log2Ratio
#761
JD12138
opened
1 year ago
2
CNVKit 0.9.9 Batch mode not producing CNS
#760
tbaker18
closed
1 year ago
2
CNVkit coverage takes too long on CRAM file
#759
looxon93
opened
1 year ago
1
cnvkit.py batch - no .cns file
#758
AndreaG5
closed
1 year ago
0
how to make CNVkit use a defined local Version of R/ Rscript in a local install
#757
claus-h-g
closed
1 year ago
2
changing ploidy values do not change call outcomes
#756
CKZan
opened
1 year ago
3
`--access` option resulted in different heatmap
#755
227BaronChen
opened
1 year ago
1
How to loop over samples cnvkit.py batch
#754
AndreaG5
opened
1 year ago
4
Add 'GC fraction for bad bins masking' to PARAMS
#753
tetedange13
closed
1 year ago
3
Extreme GC Fraction filter - mask_bad_bins - fix.py
#752
tsivaarumugam
closed
1 year ago
5
genemetrics result processing
#751
xuwanxing
opened
1 year ago
0
CNVkit can't read its own target.bed during batch command
#750
bozbezbozzel
closed
1 year ago
4
Choosing a segmentation algorithm
#749
StrawHattM
opened
1 year ago
0
Baseline building requirements
#748
pegasusCN
opened
1 year ago
0
Error using docker image for CNVkit 0.9.9 on DNAnexus
#747
mwarrier123
closed
1 year ago
1
Genemetrics only runs part way through chr1
#746
awilliams5544
closed
2 years ago
2
Use genemetrics output for calling CNV?
#745
aelhossiny
opened
2 years ago
0
interpretation of the result
#744
stroke1989
opened
2 years ago
1
method
#743
stroke1989
opened
2 years ago
1
Batch mode fails when --diagram enabled
#742
mishaprochazka
opened
2 years ago
0
Error in plotting scatter
#741
amootta
opened
2 years ago
1
Errors in fix.py
#740
wqrao
opened
2 years ago
5
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