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snakemake-workflows
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dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
MIT License
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Help with dna-seq-gatk-variant-calling
#42
Sahu-Mousumi
opened
10 months ago
0
update GitHub Actions workflow to use newer Actions versions
#41
dlaehnemann
closed
1 year ago
1
fix: update CI workflow, snakemake wrappers and python / pandas code syntax
#40
dlaehnemann
opened
1 year ago
2
TypeError in calling.smk rule merge_variants. The bwa mapping stops after creating the indexes files.
#39
ClaraApicella
opened
1 year ago
7
Mutect2
#38
radio1988
closed
1 year ago
0
Error tokenizing data. C error: Expected 5 fields in line 4, saw 6
#37
ltalignani
closed
1 year ago
2
rule plot_stats fails with "OverflowError: value too large to convert to npy_uint32"
#36
gernophil
opened
2 years ago
4
VQSR not fully implemented
#35
lczech
opened
2 years ago
4
REMOVE_DUPLICATES is false according to logs in rule mark_duplicates
#34
gernophil
opened
2 years ago
0
can't set java opts for rule recalibrate_base_qualities
#33
gernophil
opened
2 years ago
0
Choice of reference genome
#32
ThibauldMichel
opened
2 years ago
2
missing python dependency in rule plot_stats
#31
pmginacio
opened
2 years ago
2
Errors in two rules terminating run
#30
CAllex-Buckner
opened
3 years ago
2
optimizations
#29
knokknok
opened
3 years ago
0
Update README.md
#28
EQt
closed
3 years ago
0
Not executed fastqc for specified inputs
#27
nkimoto
opened
4 years ago
1
Haplotype caller with intervals runs slow
#26
vetsuisse-unibe
closed
4 years ago
2
Migrate annotation to VEP
#25
johanneskoester
closed
4 years ago
0
use latest wrappers for reference download
#24
johanneskoester
closed
4 years ago
0
update wrappers to latest release
#23
johanneskoester
closed
4 years ago
0
use peppy
#22
stolarczyk
closed
3 years ago
6
Running without known-variants
#21
silastittes
opened
4 years ago
3
Failed to open environment file mergevcfs
#20
ekarlins
closed
4 years ago
1
Failed to open environment file
#19
CharlesJB
opened
4 years ago
0
Which singularity image is used?
#18
ManavalanG
opened
4 years ago
1
Direct output to directory of interest
#17
ManavalanG
opened
4 years ago
1
Use the new workflow.inputfile handling
#16
johanneskoester
closed
4 years ago
2
obtain contigs in a lazy way, such that common.smk does not depend on…
#15
johanneskoester
closed
4 years ago
0
Migrate to github actions.
#14
johanneskoester
closed
4 years ago
0
snpeff with custom genome database
#13
RvV1979
opened
5 years ago
0
README report link served through RawGit will stop working
#12
corburn
opened
5 years ago
0
Erro in rule snpeff
#11
greenkidneybean
closed
5 years ago
1
Non-ASCII character in .py, no encoding declared
#10
greenkidneybean
closed
5 years ago
3
Output vcf.gz instead of vcf.
#9
johanneskoester
opened
5 years ago
0
Peppy
#8
vreuter
opened
5 years ago
18
Another thing. Shouldn't the project.yaml read like this for consistency:
#7
nsheff
closed
5 years ago
1
Using peppy
#6
vreuter
closed
5 years ago
1
latest release link broken
#5
kmmahan
closed
5 years ago
1
error with common.smk
#4
anjanaanilkumar1289
closed
5 years ago
12
Replace SnpEff with Annovar
#3
johanneskoester
closed
5 years ago
1
Support for panel sequencing via restriction to sites.
#2
johanneskoester
closed
5 years ago
0
removed duplicated subtitle
#1
wdecoster
closed
6 years ago
1