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HKU-BAL
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ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
BSD 3-Clause "New" or "Revised" License
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Question: Distributing ClairS
#43
dmaziec
closed
1 week ago
2
updated code for supporting ClairS SSRS training
#42
JasonCLEI
closed
1 week ago
0
Benchmarks for compute resources
#41
awgymer
opened
1 week ago
1
somatic SNV/InDel number is too many
#40
DayTimeMouse
opened
2 weeks ago
1
about v0.4.0 for calling indel
#39
DayTimeMouse
closed
2 weeks ago
1
Added BQ jittering
#38
JasonCLEI
closed
1 month ago
0
Added BQ jittering
#37
JasonCLEI
closed
1 month ago
0
Very few somatic variants in output VCF
#36
mdehankar3
closed
1 month ago
1
NumPY error when installed thru singularity and conda
#35
ccbruels
opened
2 months ago
1
Only 1 somatic variant returned
#34
Jiayi-Wang-Joey
closed
1 month ago
2
Question: Timeline for releasing new models
#33
lucy924
closed
1 month ago
4
Loci file /opt/conda/envs/clairs/bin/cnv_data/reference_files/loci_files/G1000_loci_hg38_chr1.txt does not appear to exist.
#32
erdikilic
closed
1 month ago
4
Update verdict module
#31
JasonCLEI
closed
4 months ago
0
Update verdict module
#30
JasonCLEI
closed
4 months ago
0
updated to v0.2.1
#29
zhengzhenxian
closed
4 months ago
0
samtools index: failed to open error
#28
DIPLOMICS-SA
closed
4 months ago
9
Adding Normal Sample GT to the VCF file
#27
bcantarel
closed
4 months ago
3
V1.0.0
#26
zhengzhenxian
closed
6 months ago
0
ClairS quits with exit code 0 but no output, no error logged
#25
nparmalee
closed
4 months ago
5
tmp folders not being deleted after calling
#24
A-Goretsky
closed
7 months ago
2
ClairS crashing with spaces in input file name
#23
RenzoTale88
closed
4 months ago
2
Enhancing somatic variant calling and execution speed
#22
sloth-eat-pudding
closed
4 months ago
5
Question in training data label generation code - get_candidates.py
#21
quito418
closed
8 months ago
2
sh files for data preprocessing
#20
shiying-sxu
closed
7 months ago
1
add v4.3.0 model for clair3 params
#19
bakeronit
closed
7 months ago
6
Questions Regarding Heterozygous Variants, Somatic Mutations, and Phasing in ClairS Usage
#18
sloth-eat-pudding
closed
4 months ago
4
[Inquiry for train dataset generation procedure]
#17
quito418
closed
12 months ago
2
Update run_clairs
#16
cjalder
closed
1 year ago
1
[Ask for insights on Illumina results regarding ClairS workflow/design choices]
#15
quito418
closed
1 year ago
5
Docker latest version
#14
husamia
closed
1 year ago
1
Question: comparison with DRAGEN Somatic
#13
husamia
closed
1 year ago
1
Germline variants present in output.vcf
#12
xingyaoc
closed
1 year ago
1
Nondeterminism in ClairS output
#11
xingyaoc
closed
1 year ago
1
question: model for 5khz data
#10
bakeronit
closed
1 year ago
4
Training for PacBio HiFi indel calling
#9
proteinosome
closed
1 year ago
11
Haplotype filtering step keep stuck
#8
tahashmi
closed
1 year ago
4
Modify run_clairs to take normal vcf as input and start there
#7
xingyaoc
closed
1 year ago
1
Option to call SNPs only
#6
xingyaoc
closed
1 year ago
1
select_hetero_snp_for_phasing breaks for contigs where no variants are found
#5
xingyaoc
closed
1 year ago
3
Bam files for SEQC2 samples
#4
KeyTals
closed
1 year ago
1
Running with singularity
#3
jaesvi
closed
1 year ago
2
Empty VCF produced by ClairS
#2
rowanhowellGE
closed
1 year ago
2
Interpreting the QUAL column
#1
zhemingfan
closed
1 year ago
2