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TRON-Bioinformatics
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covigator-ngs-pipeline
A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.
MIT License
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Update README.md
#65
johausmann
closed
4 months ago
0
Integrate ont pipeline
#64
priesgo
opened
9 months ago
1
Different pangolin lineages given variant caller
#63
GoncheDanesh
opened
11 months ago
0
Add mamba support and update pangolin lineage determination
#61
johausmann
closed
12 months ago
1
Update pangolin version in pipeline
#60
johausmann
closed
12 months ago
0
Update README.md
#59
johausmann
closed
1 year ago
0
Check PR on nanopore in pipeline
#58
priesgo
opened
1 year ago
0
Produced VCFs are claimed to be malformed by IGV
#57
priesgo
opened
1 year ago
2
Mamba support
#56
johausmann
closed
12 months ago
0
ENH: Add Nextclade for phylogenetic informed QC
#55
corneliusroemer
opened
1 year ago
1
Implemented lineage only mode
#54
johausmann
closed
1 year ago
1
52 restore conda compatibility with newer nextflow versions
#53
johausmann
closed
1 year ago
0
Support for conda
#52
johausmann
closed
1 year ago
0
Pangolin only mode
#51
johausmann
closed
1 year ago
0
49 add subworkflow snpeff custom genome
#50
johausmann
closed
1 year ago
1
Create a nextflow subworkflow that prepares a given reference given a FASTA and a GFF (indexing + snpEff)
#49
priesgo
closed
9 months ago
0
Update documentation with need of providing GFF file for phasing
#48
priesgo
closed
9 months ago
0
Add documentation for setting up SnpEff for custom reference
#47
priesgo
closed
9 months ago
0
Update documentation for custom reference to BWA mem2
#46
priesgo
closed
9 months ago
0
ONT sequencing data
#45
smanfri
closed
9 months ago
3
add bcftools sort operation
#44
priesgo
opened
1 year ago
0
add back in annotation of homoplasmic sites
#43
priesgo
closed
1 year ago
1
Introduce low quality clonal variants + change thresholds
#42
priesgo
closed
1 year ago
0
Filter out indels at ends of genome (especially relevant for FASTAs... use homoplasmic regions from DeMaio)
#41
priesgo
closed
1 year ago
0
pipe annotation and bgzip to save writing to disk
#40
priesgo
closed
1 year ago
0
avoid unnecessary last bgzip standalone step to improve performance
#39
priesgo
closed
1 year ago
0
add option to run pipeline on input VCF
#38
priesgo
closed
1 year ago
0
Fix phasing
#37
priesgo
closed
2 years ago
0
A special variant case which phasing.py is unable to resolve
#36
Rohit-Satyam
closed
1 year ago
4
Discussion on Masking the regions with coverage less than 20X
#35
Rohit-Satyam
opened
2 years ago
6
Python tests are failing and CI environment does not capture the error
#34
priesgo
closed
2 years ago
1
Apply normalization of VCFs before `bcftools consensus` in preparation for Pangolin
#33
priesgo
closed
2 years ago
1
AttributeError: 'str' object has no attribute 'name'
#32
Rohit-Satyam
closed
1 year ago
5
Add optional arguments to BCFtools
#31
priesgo
closed
2 years ago
1
Add optional --ignore-overlaps to ivar
#30
priesgo
closed
2 years ago
1
Use the reference in mpileup to reduce FPs
#29
priesgo
closed
2 years ago
0
Improvement in Variant calling
#28
Rohit-Satyam
closed
2 years ago
5
Improve memory use
#27
priesgo
closed
2 years ago
0
In which step exactly are homoplasmic mutations taken care of
#26
Rohit-Satyam
closed
1 year ago
5
Upgrade pangolin
#25
priesgo
closed
2 years ago
0
remove references to GISAID
#24
priesgo
closed
2 years ago
0
No signature of method: java.lang.Boolean.getFileSystem() is applicable for argument types: () values: []
#23
Rohit-Satyam
closed
2 years ago
2
change domain ids i SARS-CoV-2 from interpro to pfam
#22
priesgo
closed
2 years ago
0
Add step for primer trimming with iVar
#21
priesgo
closed
2 years ago
0
Dependency for gtfparse python package is not managed from within the conda environment
#20
priesgo
closed
1 year ago
1
Improve performance
#19
priesgo
closed
2 years ago
0
Bugfix: phasing on empty VCF
#18
priesgo
closed
2 years ago
0
ARTIC primer masking
#17
fhsantanna
closed
2 years ago
9
Phasing + removal of vt from normalization + document --keep_intermediate
#16
priesgo
closed
2 years ago
1
In relation to the GATK variant call, is there a quality score recalibration step?
#15
fhsantanna
closed
2 years ago
5
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