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bioinform
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somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
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singularity submit_SomaticSeq.sh code error ?
#85
gianfilippo
closed
4 years ago
2
dockered VarScan2 issue
#84
gianfilippo
closed
4 years ago
5
dockered vardict issue
#83
gianfilippo
closed
4 years ago
11
docker error - docker: Error response from daemon: OCI runtime create failed: container_linux.go:349: starting container process caused "process_linux.go:319: getting the final child's pid from pipe caused \"EOF\"": unknown.
#82
jeongmeani
closed
4 years ago
8
Error: In training mode, there must be both true positives and false positives in the call set
#81
vymao
closed
2 years ago
21
Ranksums
#80
litaifang
closed
4 years ago
0
Some clarifications?
#79
vymao
closed
4 years ago
8
Error: In training mode, there must be both true positives and false positives in the call set.
#78
gianfilippo
closed
4 years ago
8
RealignerTargetCreator and IndelRealigner steps
#77
gianfilippo
closed
4 years ago
2
No succesful mutations?
#76
adfnih
closed
4 years ago
2
slurm vs sge
#75
cbiitbian
closed
4 years ago
12
Strelka parameters on targeted amplicon panels, single mode (only tumor sample). Using the docker file for run.
#74
evelingonzalezfeliu
closed
4 years ago
3
addsnv.py ERROR/WARNINGS: encountered error in mutation spikein; could not pileup for region
#73
gianfilippo
closed
4 years ago
5
ImportError: libcurl.so.4: cannot open shared object file: No such file or directory
#72
gianfilippo
closed
4 years ago
7
request for examples
#71
Solenyalyl
closed
4 years ago
3
somatic mutation spike in pipeline without docker
#70
gianfilippo
closed
4 years ago
6
freebayes or other callers
#69
gianfilippo
closed
4 years ago
4
Error with somaticseq_parallel.py
#68
joonlee3
closed
5 years ago
3
default processing run_somaticseq.py
#67
innerpyg
closed
5 years ago
2
Exception: LoFreq.snvs.concat.vcf.gz does not seem to be properly sorted
#66
t-neumann
closed
5 years ago
2
GATK4 Mutect2
#65
fpbarthel
closed
6 years ago
2
update somaticseq on anaconda
#64
fpbarthel
closed
4 years ago
10
Using somaticseq for somatic calls in non-human species and tumor-only mode
#63
sbamin
closed
6 years ago
4
Fastq2bam
#62
esherafat
closed
6 years ago
2
Please release a version
#61
rhpvorderman
closed
6 years ago
2
V3.nightly
#60
litaifang
closed
6 years ago
1
V3.nightly
#59
litaifang
closed
6 years ago
0
Arguments for each caller
#58
Tato14
closed
6 years ago
1
SomaticSeq for targeted panel data
#57
Tato14
closed
6 years ago
11
Normalized multiallelic indels in CombineVariants_MVJSD.indel.vcf excluded from Ensemble.tsv
#56
pkothiyal
closed
6 years ago
3
Merge Li-Tai's new change to LY branch
#55
lijingya
closed
6 years ago
0
2.7.1
#54
litaifang
closed
6 years ago
0
2.7.1
#53
lijingya
closed
6 years ago
2
SomaticSeq.Wrapper.sh should support GATK4
#52
0xaf1f
closed
6 years ago
1
Improve documentation for snakemake workflow and link from top-level README
#51
0xaf1f
closed
6 years ago
1
Snakemake corrections
#50
0xaf1f
closed
6 years ago
7
Add a Snakemake-based workflow
#49
0xaf1f
closed
6 years ago
4
Could you provide documentation on the 70 features extracted by somaticseq? Trying to better understand SomaticSeq's model
#48
kiranchari
closed
6 years ago
2
V2.7.0
#47
litaifang
closed
6 years ago
0
No sample information error
#46
mingyi-wang
closed
6 years ago
12
submitSomaticSniper: unable to open file /mnt/<path-to-RESULTS>/1/1.bed
#45
0xaf1f
closed
6 years ago
7
V2.6.0
#44
litaifang
closed
6 years ago
0
hg19 and b37
#43
mingyi-wang
closed
6 years ago
1
The format of Truth VCF files
#42
mingyi-wang
closed
6 years ago
1
V2.4.0
#41
litaifang
closed
7 years ago
0
V2.4.0
#40
litaifang
closed
7 years ago
0
add ML options
#39
litaifang
closed
7 years ago
0
V2.3.1
#38
litaifang
closed
7 years ago
0
V2.3.1
#37
litaifang
closed
7 years ago
0
V2.3.1
#36
litaifang
closed
7 years ago
0
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