snakemake-workflows dna-seq-gatk-variant-calling issues

snakemake-workflows / dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

MIT License

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issues

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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