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harvardinformatics
/
snpArcher
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
63
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30
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Interval refactor
#61
cademirch
closed
2 years ago
2
Fix conda envs
#60
tsackton
closed
2 years ago
0
Use mosdepth d4tools to facilitate coverage calcs
#59
tsackton
closed
2 years ago
0
Local reference
#58
cademirch
closed
2 years ago
0
Using local reference genomes
#57
tsackton
closed
2 years ago
6
Issue with problem intervals / gvcf2DB rule
#56
ArsenaultResearch
closed
2 years ago
2
refactoring usage of intervals
#55
tsackton
closed
2 years ago
2
Interval creation errors
#54
tsackton
closed
2 years ago
1
Callable sites rules, bugfixes, resource improvements
#53
tsackton
closed
2 years ago
0
Rerunning a species set with updating samples
#52
tsackton
closed
3 months ago
0
Gather VCFs tmp dir space
#51
tsackton
closed
2 years ago
2
Ccgp workflow2
#50
cademirch
closed
2 years ago
1
Dev
#49
tsackton
closed
2 years ago
0
Add option to download from ENA
#48
tsackton
closed
2 years ago
3
Add bedgraph computation
#47
tsackton
closed
2 years ago
0
Input function to deal with n=1 samples
#46
tsackton
closed
2 years ago
0
Dev - bring sambamba update to main
#45
cademirch
closed
2 years ago
0
Sambamba
#44
cademirch
closed
2 years ago
0
Bugfix
#43
cademirch
closed
2 years ago
0
Update test_qc.yaml
#42
cademirch
closed
2 years ago
0
Quality of Life bugfixes
#41
tsackton
closed
2 years ago
0
Quality of life improvements
#40
tsackton
closed
2 years ago
17
Updating resources
#39
tsackton
closed
2 years ago
0
Updating resources
#38
tsackton
closed
2 years ago
0
Merge mappability and some qc fixes
#37
cademirch
closed
2 years ago
0
Merging main into dev
#36
cademirch
closed
2 years ago
0
Fixing issues with test workflow
#35
tsackton
closed
2 years ago
0
change yaml to safe_load
#34
tsackton
closed
2 years ago
1
Dev
#33
cademirch
closed
2 years ago
0
Dev
#32
cademirch
closed
2 years ago
1
Bugfix
#31
sjswuitchik
closed
2 years ago
2
MarkDuplicates memory issues
#30
cademirch
closed
2 years ago
0
Create list of final data sets
#29
sjswuitchik
closed
2 years ago
0
Bugfix
#28
cademirch
closed
2 years ago
0
Set up for Workflowhub
#27
tsackton
closed
3 months ago
0
Sync dev with main
#26
tsackton
closed
2 years ago
0
Create LICENSE
#25
tsackton
closed
2 years ago
0
Dev - run script fix
#24
sjswuitchik
closed
2 years ago
2
Intervals without Ns in reference
#23
cademirch
closed
2 years ago
2
Rewrite README
#22
cademirch
closed
1 year ago
0
Make it easier for users to supply own reads and reference
#21
cademirch
closed
2 years ago
1
Merge dev updates to main
#20
tsackton
closed
2 years ago
0
Dev
#19
cademirch
closed
2 years ago
1
Delete stray file
#18
erikenbody
closed
2 years ago
1
Longer Term Roadmap
#17
tsackton
opened
2 years ago
0
Add Quality Control Outputs
#16
tsackton
closed
2 years ago
3
Automatically determine correct coverage parameters
#15
tsackton
opened
2 years ago
1
Fastqc or other fastq checks?
#14
tsackton
closed
7 months ago
0
Use Snakemake Best Practices
#13
tsackton
closed
2 years ago
3
Develop Test Datasets
#12
tsackton
closed
2 years ago
3
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