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49 Open 36 Closed
49 Open 36 Closed
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Issues list

NetMHC url error
#162 opened Nov 19, 2024 by SDSdustyF
report bug
#156 opened Jun 3, 2024 by Cosmos9526
Use NetMHC locally in pipeline
#155 opened Jan 31, 2024 by hjaysong
Relative path issue when running not in the repo directory
#151 opened Jul 12, 2022 by gongyixiao
Overriding yaml file paths using parameters in dockerless mode
#150 opened Jul 12, 2022 by gongyixiao
Failed to call strelka2
#149 opened Feb 24, 2021 by marcogao2019
docker building failed using build.sh command
#147 opened Jan 7, 2020 by joshuabhk
2
Non-parallel IndelRealigner sometimes fails
#145 opened Aug 23, 2019 by julia326
Add chimeric alignments to STAR
#144 opened Aug 9, 2019 by iskandr
Add Manta for identifying candidate larger indels
#142 opened Aug 6, 2019 by iskandr
2
Add strelka2 to pipeline
#136 opened Feb 27, 2019 by julia326
4
Make sure initial input files fully copied over
#132 opened Dec 31, 2018 by julia326
Prioritize mutect-strelka Vaxrank over mutect2 jobs
#129 opened Nov 28, 2018 by julia326
Check config file for obvious mistakes
#127 opened Oct 11, 2018 by iskandr
Long-running steps
#125 opened Sep 25, 2018 by iskandr
How do we make copy-to-gcloud.sh a part of the pipeline?
#123 opened Sep 19, 2018 by iskandr
1
Run STAR in "two pass mode" to detect novel splice junctions
#122 opened Sep 19, 2018 by iskandr
Saved unmapped RNA reads in SAM/BAM output
#121 opened Sep 19, 2018 by iskandr
QC tools for RNA and DNA
#120 opened Sep 18, 2018 by julia326
1
Alternative config format for sequencing data
#118 opened Sep 14, 2018 by iskandr
Subtract germline VCF from somatic VCFs
#109 opened Jul 27, 2018 by iskandr
Prepare Kallisto quantification for CIBERSORT
#105 opened Jul 18, 2018 by iskandr Broader profiling and interpretation of the tumor's mutations
@timodonnell
4
Try running POLYSOLVER
#104 opened Jul 18, 2018 by iskandr Broader profiling and interpretation of the tumor's mutations
Generate Immunophenogram visualization
#102 opened Jul 18, 2018 by iskandr Broader profiling and interpretation of the tumor's mutations
Make expected config YAML instead of JSON
#96 opened Jun 27, 2018 by julia326
1
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