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mtandon09
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CCBR_GATK4_Exome_Seq_Pipeline
An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
https://mtandon09.github.io/CCBR_GATK4_Exome_Seq_Pipeline/
MIT License
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Unified freec fix
#35
skchronicles
closed
2 years ago
0
Dry-run issue with Snakemake Version 7.7.0
#34
skchronicles
opened
2 years ago
1
Added VQSR rule and config for cluster
#33
dnousome
closed
2 years ago
1
--wait option added for HPCAPI orchestration
#32
kopardev
closed
2 years ago
0
Adding trigger to manually trigger rebuilding of docs
#31
skchronicles
closed
2 years ago
0
Cache DockerHub images locally
#30
skchronicles
closed
2 years ago
0
Patch: BCF tools in SOB Detection rule
#29
skchronicles
closed
2 years ago
0
May the FRCE be with you
#28
skchronicles
closed
2 years ago
0
Update Dockerfile
#27
dnousome
closed
2 years ago
5
Adding script to create reference genome resource bundles
#26
skchronicles
closed
2 years ago
0
Adding docker pull badge
#25
skchronicles
closed
2 years ago
0
vcf2maf: VEP release 102 changes
#24
skchronicles
closed
2 years ago
0
New README and updating example run sub command
#23
skchronicles
closed
2 years ago
0
First draft of pipeline documentation
#22
skchronicles
closed
2 years ago
1
Consolidating reference files and pipeline resources
#21
skchronicles
closed
2 years ago
0
vcf2maf updates
#20
skchronicles
closed
2 years ago
1
Fixes for CNV and FFPE rules
#19
skchronicles
closed
2 years ago
2
Updates and bug fixes
#18
skchronicles
closed
2 years ago
0
Converting remaining SNP calling, FFPE, and QC rules
#17
skchronicles
closed
3 years ago
0
Converting remaining SNP calling, QC, and FFPE rules
#16
skchronicles
closed
3 years ago
0
Converting Somatic SNP calling rules for TN pairs
#15
skchronicles
closed
3 years ago
0
Converting CNV and preprocessing rules
#14
skchronicles
closed
3 years ago
0
Mutect/1.1.7 Dockerfile
#13
skchronicles
closed
3 years ago
0
Adding python/2.7, strelka/2.9.10, manta/1.6.0 and VarDict/1.8.2 to b…
#12
skchronicles
closed
3 years ago
0
Adding snpEff and samblaster to base docker image
#11
skchronicles
closed
3 years ago
0
Updating base image and converting germline rules
#10
skchronicles
closed
3 years ago
0
Base image dockerfile
#9
skchronicles
closed
3 years ago
0
Incorporating QC docker images
#8
skchronicles
closed
3 years ago
0
Fix: avoid hanging process with empty input files in MAF combination …
#7
skchronicles
closed
3 years ago
0
GATK4 WES 2.X Pipeline
#6
skchronicles
closed
3 years ago
0
Merge with main
#5
mtandon09
opened
3 years ago
0
Update run.sh
#4
dnousome
closed
3 years ago
0
Add mouse tumor normal pipeline and fixed slurm output filenames
#3
dnousome
opened
3 years ago
0
Revert "Merge pull request #1 from mtandon09/main"
#2
ashishjain1988
closed
3 years ago
0
Merge pull request #1 from mtandon09/main
#1
ashishjain1988
closed
3 years ago
0