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Issues list

where can I modify the docker container "/opt/somaticseq/somaticseq" to "/opt/somaticseq-3.10.0/somaticseq"
#138 by ddzhang3 was closed Jan 27, 2025
23
makeSomaticScripts.py "single" generated command incorrectly passes vcf.gz file to option -d of lofreq call.
#134 by harrymatthews50 was closed Jun 29, 2024
2
Error when running FFPE training data from SEQ2C
#130 by GACGAMA was closed Jan 30, 2024
5
how to obtain all variants where the "FILTER" column is not labeled as "PASS"
#128 by xiechangxiao was closed Dec 5, 2023
1
UnboundLocalError: cannot access local variable 'normal_name' where it is not associated with a value
#127 by SAADAT-Abu was closed Jan 25, 2024
10
Error when running makeSomaticScripts with multiple threads
#125 by GACGAMA was closed Aug 8, 2023
3
Dockerized alignment workflow does not work with multiple input files
#124 by GACGAMA was closed Aug 2, 2023
5
Applying internal filters to outputs before running SomaticSeq
#123 by ronkesm was closed Jan 25, 2024
1
somaticseq failing for same command it had previously successfully run
#122 by csreej27 was closed Jan 25, 2024
11
Ground Truths required for training
#121 by harish0201 was closed Jun 21, 2023
1
Where are the 10x Genomics single-cell copy number variation (CNV) analysis results?
#120 by genetronhealth was closed May 10, 2023
7
Question for the paper on establishing the reference call set
#119 by FriederikeHanssen was closed Apr 7, 2023
3
Somaticseq makeSomaticScripts.py running and output issues
#117 by csreej27 was closed Apr 7, 2023
8
SEQC2: Some high confidence SNVs and INDELs in VCF are outside of regions defined by High-Confidence_Regions_v1.2.bed
#116 by luederm was closed Oct 21, 2022
2
Docker issue with latest version
#115 by emucaki was closed Oct 21, 2022
1
Pretrained Classifier
#114 by kokyriakidis was closed Jul 28, 2022
3
Question about simulating somatic mutations
#113 by leedchou was closed Jul 28, 2022
7
Special setting for b37?
#112 by yoda0612 was closed Apr 11, 2022
14
Result of TNscope caller
#111 by yoda0612 was closed Mar 26, 2022
4
Filter truth vcf files for dbsnp?
#110 by iserf was closed Mar 26, 2022
1
somatic_xgboost.py train: xgboost.core.XGBoostError
#109 by iserf was closed Mar 16, 2022
SV truthset for SEQC
#108 by miyakokodama was closed Mar 21, 2022
1
makeSomaticScripts.py single mode passing certain arguments
#107 by dnousome was closed Mar 2, 2022
2
generating training data using single medium-coverage replicate of normal sample
#106 by kiranchari was closed Feb 6, 2022
1
must the mutation spike-in singularity pipeline be processed in a single HPC run?
#105 by kiranchari was closed Dec 28, 2021
2
ProTip! no:milestone will show everything without a milestone.