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TrinityCTAT
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ctat-mutations
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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Not able to run CTAT Mutations
#135
mariasolruiz
opened
1 month ago
24
mutation-lib supplement for GRCm39
#134
cachedpotato
opened
3 months ago
10
fix the disk space for long read in SplitNCigarReads
#133
qinqian
closed
2 months ago
0
hg19 igv report html appears broken (works fine for hg38 though)
#132
brianjohnhaas
opened
3 months ago
0
dbSNP frequence question
#131
teresa1997
opened
5 months ago
1
Missing path to CTAT_GENOME_LIB
#130
teresa1997
opened
7 months ago
5
Issue with BQSR maximum cycle value
#129
irzamsarfraz
opened
7 months ago
1
k8 missing from Container
#128
readline
closed
9 months ago
5
allow for igv-reports if filtering set to none
#127
brianjohnhaas
opened
9 months ago
0
Annotate CRAVAT error
#126
gianfilippo
opened
10 months ago
18
Update Docker file for compatibility with nextflow
#125
CloXD
closed
1 year ago
1
zipfile.BadZipFile: File is not a zip file
#124
wx904
opened
1 year ago
3
Annotating VCF at BLAT ED
#123
shivUSF
opened
1 year ago
8
Not enough memory for BAM sorting
#122
taot2007
opened
1 year ago
5
Annotate Cravat step can not read file
#121
shivUSF
closed
1 year ago
12
Do I need spliced fastq?
#120
HyojeenLee
opened
1 year ago
0
AWS EC2 + docker and issue of cromwell or STAR
#119
HyojeenLee
opened
1 year ago
5
HaplotypeCaller - Intervals option
#118
gremame
opened
1 year ago
9
update index issue
#117
brownmp
closed
1 year ago
0
fix issue with indexing error
#116
brownmp
closed
1 year ago
0
Update annotate_PASS_reads.py
#115
brownmp
closed
1 year ago
1
updates to WDL
#114
brownmp
closed
1 year ago
0
Update annotate_PASS_reads.py
#113
brownmp
closed
1 year ago
0
pipeline extremely slow: stuck at "Annotate PASS Reads"
#112
gianfilippo
closed
1 year ago
40
Could not run the test sample using ctat-mutations
#111
DecodeGenome
opened
1 year ago
3
subprocess.CalledProcessError
#110
min0609
opened
1 year ago
12
CTAT mutations V3.2.0 running error with example data
#109
hungying
closed
2 years ago
2
Localization via hard link has failed:
#108
vzupan3
closed
2 years ago
5
RNAEditing Analysis
#107
kokyriakidis
opened
2 years ago
17
File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd)
#106
yuanqingyan
opened
2 years ago
4
After "WaitingForReturnCode ", pipeline stuck
#105
jaewon-cho
opened
2 years ago
4
ctat-mutations-WorkflowFailedState
#104
taot2007
opened
2 years ago
5
internet connection error
#103
jianbiaoli
opened
2 years ago
5
question about the outputs
#102
jaewon-cho
opened
2 years ago
2
errors in mutation lib integration
#101
aoifgri
opened
2 years ago
5
Interoperability between CTAT tools
#100
tjbencomo
closed
2 years ago
2
Devel
#99
brianjohnhaas
closed
2 years ago
0
unrecognized parameter name "genomeType" in input "genomeParameters.txt"
#98
jeongmeani
opened
2 years ago
1
information about SNV annotation
#97
ConcettaDe4
opened
3 years ago
0
REDIportal V2.0 update
#96
kokyriakidis
opened
3 years ago
1
capture ED memory increase
#95
brianjohnhaas
closed
3 years ago
0
error on testing set
#94
ConcettaDe4
opened
3 years ago
8
changing tmp directory of singularity image
#93
ConcettaDe4
opened
3 years ago
2
Terra configuration
#92
jbeane0428
opened
3 years ago
1
EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"
#91
jbeane0428
opened
3 years ago
8
add multithreading for the variant annotation steps of the workflow
#90
brianjohnhaas
closed
3 years ago
0
added support for --variant_ready_bam to skip over all the bam proces…
#89
brianjohnhaas
closed
3 years ago
0
overly verbose Checkpointing info logging msgs
#88
brianjohnhaas
closed
3 years ago
0
EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"
#87
YingYa
opened
3 years ago
3
gatk CreateSequenceDictionary command issue
#86
readline
closed
3 years ago
10
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