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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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added RVBLR (rvboost-like-R) to ctat mutations pipe
#39
brianjohnhaas
closed
4 years ago
0
Added progress bar to monitor status
#38
brownmp
closed
4 years ago
1
rna-editing annotations not as comprehensive on GRCh38 vs hg19
#37
brianjohnhaas
opened
4 years ago
0
cancer tab fields deprecated
#36
brianjohnhaas
closed
4 years ago
0
Fixed MuPIT link
#35
brownmp
closed
4 years ago
0
KeyError: u'Mutation ID'
#34
maojn
closed
4 years ago
11
bugfix - param varnames didnt match for mutect2 call
#33
brianjohnhaas
closed
5 years ago
0
variant allele freq and multi-mapping read annotations
#32
brianjohnhaas
closed
5 years ago
0
Update the check to see if running in conda environment
#31
brownmp
closed
5 years ago
0
updated fucntion generate_GetPileupSummaries_cmds
#30
brownmp
closed
5 years ago
0
Fixed the output of fastaFromBed by indexing
#29
brownmp
closed
5 years ago
1
minor updates, capturing primary outputs with filenames reflecting mode for var detection
#28
brianjohnhaas
closed
5 years ago
0
major revision - annotate instead of filter
#27
brianjohnhaas
closed
5 years ago
0
add multi-mapping and read pass annotations
#26
brownmp
closed
5 years ago
1
repeat element and exon splice adjacency annotation utilities added
#25
brianjohnhaas
closed
5 years ago
0
converting PE reads to SE reads before dup marking
#24
brianjohnhaas
closed
5 years ago
0
Changed the order of steps (snpeff before dbsnp), and changed rna_edi…
#23
brownmp
closed
5 years ago
0
updates for docker and singularity testing
#22
brianjohnhaas
closed
5 years ago
0
further overhaul of ctat mutations pipe, including parallelization
#21
brianjohnhaas
closed
5 years ago
0
Simple
#20
vrushali-broad
closed
5 years ago
1
Simplified pipeline in devel
#19
vrushali-broad
closed
5 years ago
0
Simplified Pipeline
#18
vrushali-broad
closed
5 years ago
0
Devel
#17
brianjohnhaas
closed
5 years ago
0
refGene.sort.bed creation support
#16
brianjohnhaas
closed
5 years ago
0
04/02/19
#15
vrushali-broad
closed
5 years ago
0
igv_reports module use
#14
brianjohnhaas
closed
5 years ago
0
No sciedpiper
#13
brianjohnhaas
closed
5 years ago
0
updated makefile to run both tests
#12
brianjohnhaas
closed
5 years ago
0
BAM Index file
#11
asmariyaz23
closed
5 years ago
0
COSMIC pulling CANCER snps in cancer.vcf
#10
vrushali-broad
closed
5 years ago
0
Viz int
#9
asmariyaz23
closed
5 years ago
0
reorganized menu and updated test data
#8
brianjohnhaas
closed
6 years ago
0
need full path to plugins dir
#7
brianjohnhaas
closed
6 years ago
0
updates for script locations and py3 compat
#6
brianjohnhaas
closed
6 years ago
0
updates for py3 and localizing included scripts
#5
brianjohnhaas
closed
6 years ago
0
wiki documentation
#4
brianjohnhaas
closed
4 years ago
1
move documentation to wiki
#3
vrushali-broad
closed
4 years ago
0
mutation pipeline to run off CTAT genome lib
#2
vrushali-broad
closed
4 years ago
0
add Docker support
#1
vrushali-broad
closed
4 years ago
0
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