issues
search
cortes-ciriano-lab
/
savana
Somatic structural variant caller for long-read data
Apache License 2.0
41
stars
2
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Should the input bam be phased?
#45
ywzhang071394
closed
1 week ago
1
working of savana cna calling
#44
sachingadakh
closed
1 week ago
1
--cn_binsize is a required argument for the main/default savana process
#43
TBradley27
closed
1 week ago
1
Unavailibility of normal tissue sample
#42
sachingadakh
closed
1 week ago
1
Field index out of range
#41
jakelee0711
closed
1 week ago
1
BrokenPipeError: [Errno 32] Broken pipe
#40
ywzhang071394
closed
1 week ago
3
utf-8 error
#39
selmapichot
closed
4 months ago
0
Undetected reads in normal tissue
#38
apsteinberg
opened
5 months ago
3
Bugfix for classification when an SV type is not present
#37
helrick
closed
6 months ago
0
might it work on a Mac?
#36
proukakis
closed
4 days ago
1
Query About Training SAVANA with CLR Data for Improved Results
#35
LayalYasin
closed
4 days ago
1
Request for additional parameters for a higher precision on somatic variant callsets
#34
andyjslee
closed
1 month ago
2
Variant with POS=0 in savana vcf output
#33
waltergallegog
closed
4 days ago
1
Merging changes into stable refactoring branch
#32
helrick
closed
10 months ago
0
Dataset of true somatic SVs used for savana training
#31
waltergallegog
closed
4 days ago
1
Savana performance on the Valle-Inclan benchmark
#30
waltergallegog
closed
4 days ago
1
bumping version for bioconda linter (related to #27)
#29
helrick
closed
11 months ago
0
What does running SAVANA with ONT_noisy imply?
#28
MartinezRuiz-Carlos
closed
4 days ago
1
ValueError: node array from the pickle has an incompatible dtype
#27
waltergallegog
opened
11 months ago
4
Questions Regarding the SV types and their associations
#26
yashcrux
opened
1 year ago
0
Failed to read reference bug
#25
zhemingfan
closed
1 year ago
4
Fix for classifying mate of breakend
#24
helrick
closed
1 year ago
0
KeyError cram support
#23
kcleal
closed
1 year ago
3
No deletions, inversions, translocations called by the caller
#22
yashcrux
closed
1 year ago
9
Small and possibly erroneous SVs in the final strict VCF file
#21
zhemingfan
closed
1 year ago
2
ValueError raised when aligned with NGMLR
#20
lingchenL
opened
1 year ago
1
No read depth
#19
Akazhiel
closed
1 year ago
1
add INSSEQ info for inserted_sequence
#18
soymintc
opened
1 year ago
10
No records reported with tumor support lower than 6
#17
waltergallegog
closed
4 days ago
6
Include savana command in vcf output
#16
waltergallegog
closed
1 year ago
1
SAVANA v1.0.0
#15
helrick
closed
1 year ago
2
Sort output VCF files
#14
helrick
closed
1 year ago
0
SVLEN INFO field should be negative for deletions
#13
waltergallegog
closed
1 year ago
2
VCF Updates
#12
helrick
closed
1 year ago
0
fixing rounding bug (#10)
#11
helrick
closed
1 year ago
0
Bug: rounding error when stat value is None
#10
helrick
closed
1 year ago
0
Refactor code to prepare for filtering improvements
#9
helrick
closed
1 year ago
0
Add SVTYPE in the INFO column
#8
soymintc
closed
1 year ago
2
Label VCF and output files with sample name
#7
helrick
closed
1 year ago
0
README updates
#6
helrick
closed
1 year ago
0
Fixes for bioconda build and checks
#5
helrick
closed
1 year ago
0
Create setup.py in order for SAVANA to be conda-installable
#4
helrick
closed
1 year ago
0
publish savana on conda
#3
helrick
closed
1 year ago
1
Fixing bugs identified with the install of SAVANA
#2
helrick
closed
1 year ago
0
adding strict/lenient VCF output file filters for somatic variants
#1
helrick
closed
1 year ago
0