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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 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
Update master for 3.0.0
#85
joshua-gould
closed
3 years ago
0
Added encoding option to opening file.
#84
brownmp
closed
3 years ago
0
Fix the issue when GT_1/2 is not present in RVBLR
#83
brownmp
closed
3 years ago
0
Updated boosting. Addressed the situation if no variants or a single …
#82
brownmp
closed
3 years ago
0
Mutations in DEMO data not found
#81
neoscreen
opened
3 years ago
5
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9
#80
esebesty
closed
3 years ago
5
Fix the tmp.vcf.gz to tmp.vcf when using hard filtering.
#79
brownmp
closed
3 years ago
0
Reset Cancer Filter Variants to True
#78
brownmp
closed
3 years ago
0
Devel
#77
brownmp
closed
3 years ago
0
check if input vcf is gzipped. Check if no variants to annotate
#76
joshua-gould
closed
3 years ago
0
Updated RVBLR. Added option to run on SNPs and INDELs separately.
#75
brownmp
closed
3 years ago
0
updated boosting script and splitting snps/indels
#74
brownmp
closed
3 years ago
0
added additional boosting options
#73
brownmp
closed
3 years ago
0
Devel
#72
brownmp
closed
3 years ago
0
Added errors='ignore' to ignore unicode utf-8 conversion
#71
joshua-gould
closed
3 years ago
0
update boosting option
#70
brownmp
closed
3 years ago
0
Commented out monitoring script used for profiling. Added read_var_pos_annotation_cpu argument.
#69
joshua-gould
closed
3 years ago
0
Added option to pass additional options to haplotype caller. Added option to toggle mark dups.
#68
joshua-gould
closed
3 years ago
0
Wdl
#67
joshua-gould
closed
3 years ago
0
Updated to work locally or on Terra. Simplified command line arguments.
#66
joshua-gould
closed
3 years ago
0
Fixed removing files. Added script for monitoring resource usage.
#65
joshua-gould
closed
3 years ago
0
clean up downloaded tar files and tools used for installation (git). Include 200MB cromwell jar file.
#64
joshua-gould
closed
3 years ago
0
Converted pipeline to WDL
#63
joshua-gould
closed
3 years ago
1
Added option to take bed file in directly instead of lib dir
#62
joshua-gould
closed
3 years ago
0
create_report: command not found
#61
IvantheDugtrio
closed
3 years ago
4
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346: invalid continuation byte
#60
foxchase
closed
4 years ago
3
Supplementary lib doesn't contain gnomad-lite.vcf.gz file and the demo run crashes
#59
alina-shitrit
opened
4 years ago
9
Testing done on Regressors
#58
vrushali-broad
closed
4 years ago
0
Devel
#57
vrushali-broad
closed
4 years ago
0
Mutation expected not found
#56
afaissa
opened
4 years ago
7
needs R installed in Docker for boosting
#55
brianjohnhaas
closed
3 years ago
1
include PoN
#54
brianjohnhaas
opened
4 years ago
0
optionally add normal dna vcf mask
#53
brianjohnhaas
opened
4 years ago
0
CTAT-mutations-program
#52
ryangimple
opened
4 years ago
14
CTAT-mutation-lib-integration
#51
ryangimple
opened
4 years ago
6
Integrate open-cravat. Fixed display of cosmic id in igv report
#50
joshua-gould
closed
4 years ago
0
allow multiple filtering methods
#49
brianjohnhaas
opened
4 years ago
0
rerun cancer annotations based on each filtering strategy
#48
brianjohnhaas
opened
4 years ago
0
cosmic id not showing up in mutation inspector html report
#47
briandiamondage-sema4
opened
4 years ago
0
Error, a STAR genome index must be provided for the STAR alignment and isn't being found
#46
shellyxun
closed
4 years ago
1
updated the RVBLR R script
#45
brownmp
closed
4 years ago
0
needs to work w/ single-end rna-seq data
#44
brianjohnhaas
closed
4 years ago
1
pctextpos into rvblr
#43
brianjohnhaas
closed
4 years ago
0
PctExtPos and annot_PASS_reads on by default
#42
brianjohnhaas
closed
4 years ago
0
Cosmic hg 19 vcf in CTAT Mutation Lib Supplement for hg 38.
#41
ruslan-abasov
closed
4 years ago
3
Containers missing Perl module "URI::Escape"
#40
seb45tian
closed
4 years ago
3
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