artic-network fieldbioinformatics issues

artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline

MIT License

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issues

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PyVCF assigns a QUAL value of '.' instead of zero

#134 knewl opened 4 months ago
0
htslib =1.17 dependency PLEASE UPDATE

#133 robertwhbaldwin opened 4 months ago
1
Error: bcftools consensus fail with overlapping variants

#132 arianna-smith opened 4 months ago
5
Custom bed file with "primer gaps" causes workflow to crash at artic-tools vcf_checker step

#131 DABAKER165 closed 7 months ago
1
Conda environment set up

#130 zkkhalil opened 9 months ago
3
Clarify what's meant by 'Suppress variant'

#129 smsaladi opened 9 months ago
0
KeyError: 'SupportFraction' when running margin_cons.py

#128 GammaCarbon7 opened 9 months ago
0
Update medaka version

#127 laura-bankers closed 10 months ago
2
Artic v5 mismatched primer names in bedfile causes "dropped" amplicons

#126 Sam-Sims closed 10 months ago
1
Overlapping variants in fail.vcf and pass.vcf cause preconsensus to be masked and thus bcftools complains when applying the "pass" variant

#125 Sam-Sims opened 1 year ago
2
no version information available (required by samtools)

#124 alexahess opened 1 year ago
5
Update vcftagprimersites.py

#123 mattloose closed 10 months ago
0
Conda recipe for 1.2.3 not working

#122 tavareshugo closed 1 year ago
8
pipeline has stopped working...!

#121 rebeelouise opened 1 year ago
5
What is the default mindepth ?

#120 Hugsh closed 1 year ago
4
artic_vcf_merge Fails

#119 Rohit-Satyam closed 1 year ago
2
Fix align_trim:find_primer

#118 boospooky opened 1 year ago
1
fix: update longshot to avoid intermittent `thread 'main' panicked at 'assertion failed: p <= 0.0'` error

#117 KatSteinke closed 1 year ago
1
Unable to install artic on mac

#116 Rosina-Codes opened 1 year ago
0
Error with medaka consensus

#115 lqhungpt closed 1 year ago
1
vcf_filter.py filtering parameters and align_trim.py for alternative primer scheme

#114 kakuk9 opened 1 year ago
0
fix: Ignore bases outside the reference

#113 RenanWA opened 2 years ago
0
feat: make flag -A in Longshot optional

#112 RenanWA opened 2 years ago
0
Fix align_trim to deal with long deletion containing left primer

#111 hsnguyen opened 2 years ago
0
bugfix: bcftools overlapping variants issue

#110 rzlim08 opened 2 years ago
0
Longshot `thread 'main' panicked at 'assertion failed: p <= 0.0'` error: possible to update longshot?

#109 KatSteinke closed 1 year ago
3
artic pipeline not installing properly: ModuleNotFoundError: No module named 'importlib.metadata'

#108 aduton2000 closed 2 years ago
1
SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

#107 thomasbtf closed 2 years ago
3
issue assigning variants occuring within an amplicon overlap region

#106 george-githinji opened 2 years ago
3
Muscle 5.1 breaks the excution of `artic minion`

#105 pdp10 closed 2 years ago
6
v1.2.2

#104 BioWilko closed 2 years ago
0
Artic_vcf_merge failed

#103 idolawoye closed 2 years ago
2
artic minion fails with midnight primers

#102 rzlim08 closed 1 year ago
1
Question: read group assignment in align_trim

#101 gianfilippo opened 2 years ago
1
Medaka calls a 5 nt deletion instead of a 6 nt deletion

#100 MarieLataretu opened 2 years ago
1
Question regarding align_trim.pl

#99 ARastrojo opened 2 years ago
7
V1200/midnight primer scheme

#98 rebeelouise opened 2 years ago
1
Deletion no longer being called

#97 cpmorris82 opened 2 years ago
0
Could not find primer scheme

#96 amv33576 opened 2 years ago
1
EPI2ME ARTIC failing for Midnight primers

#95 MMitali13 opened 2 years ago
1
Variant in amplicon overlapping region

#94 hannahgoldswain opened 2 years ago
2
artic_get_stats fails because V4 primer names in align_trim report don't match names in .bed file

#93 KatSteinke closed 2 years ago
1
SNP filtering/masking/soft clipping with medaka

#92 shimbalama opened 2 years ago
0
Error when running with too few reads/very low coverage

#91 Coppini opened 2 years ago
3
How do deal with overlapping mutations in pass.vcf and fail.vcf?

#90 rpetit3 opened 2 years ago
0
quality Filter for pass.vcf

#89 pratibha-kadam opened 2 years ago
0
artic-tools check_vcf Segmentation fault on empty VCF files

#88 rdeborja opened 2 years ago
5
Installation with conda

#87 rebeelouise closed 2 years ago
1
add option to skip muscle

#85 emalorkova opened 2 years ago
0
Artic-network for Aarch64 system

#84 hanfan1803 opened 3 years ago
0