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harvardinformatics
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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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update docs about profiles
#205
cademirch
closed
2 days ago
0
merge
#204
cademirch
closed
3 days ago
0
Error running the code
#203
AmitSharma267
opened
3 days ago
5
Invalid --distribution specification?
#202
brantfaircloth
closed
3 days ago
3
Error in rule sort_gatherVcfs
#201
daicy527
closed
4 days ago
2
Error with running the command
#200
AmitSharma267
closed
3 days ago
2
Postprocessing update
#199
erikenbody
closed
4 days ago
0
Error with big dataset and slurm
#198
max-hence
opened
2 weeks ago
4
AttributeError
#197
OsmanthusZhang
opened
3 weeks ago
3
fastq.smk
#196
atigano
closed
4 weeks ago
2
qc html
#195
jasonwjohns
opened
4 weeks ago
4
concat json fastp summary
#194
cademirch
closed
4 weeks ago
0
Collect fastp stats fails for samples with multiple runs per BioSample
#193
tsackton
closed
4 weeks ago
3
make gls work again. fix minor issues with non-intervals. update docs
#192
cademirch
closed
1 month ago
0
running QC module
#191
jasonwjohns
opened
1 month ago
6
Adding additional samples to pipeline
#190
ruthrivkin
opened
1 month ago
2
Fix snp summary
#189
erikenbody
closed
1 month ago
0
add config option to sort reads with bbmap before read trimming
#188
erikenbody
closed
1 month ago
0
Rule Exception in rule bam2gvcf - Attribute error
#187
spilornis-ng
closed
1 month ago
3
feature request: give a bcftools option
#186
andrewkern
opened
1 month ago
1
concat_gvcfs error
#185
jasonwjohns
closed
1 month ago
9
use json summary from fastp to make sure all stdout/stderr goes to log
#184
cademirch
closed
1 month ago
0
Error in rule fastp
#183
spilornis-ng
closed
1 month ago
2
Key Error: workflow/rules/common.smk, line 25: 'resource_config'
#182
Erythroxylum
closed
1 month ago
6
Fix stray resource configs, sentieon issues
#181
cademirch
closed
1 month ago
0
KeyError while setting up dry run
#180
spilornis-ng
closed
1 month ago
1
add mark dups option
#179
cademirch
closed
2 months ago
0
fix docs
#178
cademirch
closed
2 months ago
0
fix docs
#177
cademirch
closed
2 months ago
0
slurm command not appearing on docs page
#176
jasonwjohns
closed
2 months ago
3
Feat bcftools norm
#175
cademirch
closed
2 months ago
0
bcftools norm for issue#163
#174
cademirch
closed
2 months ago
0
Feat optional dedup
#173
cademirch
closed
2 months ago
0
Question: Can I disable MarkDuplicates?
#172
Erythroxylum
closed
2 months ago
11
Harvardinformatics snakemake7
#171
cademirch
closed
2 months ago
0
Support Snakemake>8.0
#170
cademirch
closed
2 months ago
8
merge main
#169
cademirch
closed
2 months ago
0
Admixture contig names
#168
erikenbody
closed
3 months ago
0
fix issue with qc-dashboard on different filesystems
#167
cademirch
closed
3 months ago
0
Warning rule qc_qc_plots stops the pipeline
#166
ffertrindade
closed
3 months ago
2
sambamba error
#165
jasonwjohns
closed
3 months ago
11
Update setup.md
#164
cademirch
closed
3 months ago
0
option for allele merging - VCF2TileDBException
#163
gghill
closed
2 months ago
7
remove --overwrite from tar. incompatible with bsdtar, is default for…
#162
cademirch
closed
3 months ago
0
issues with packages for creating enviornment
#161
jasonwjohns
closed
3 months ago
13
KeyError in file
#160
weirdo-onlooker
closed
3 months ago
4
Remove fastq and bam files
#159
max-hence
closed
3 months ago
2
encountered same error when setting cores and executing snpArcher on my local machine
#158
yuan-circle-long
closed
3 months ago
6
Add resources to rules
#157
tsackton
closed
4 months ago
0
Are genotype likelihoods available?
#156
Erythroxylum
closed
4 months ago
1
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