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36 Open 34 Closed
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Issues list

PyVCF assigns a QUAL value of '.' instead of zero
#134 opened Mar 6, 2024 by knewl
htslib =1.17 dependency PLEASE UPDATE
#133 opened Feb 20, 2024 by robertwhbaldwin
1
Error: bcftools consensus fail with overlapping variants
#132 opened Feb 16, 2024 by arianna-smith
5
Conda environment set up
#130 opened Oct 6, 2023 by zkkhalil
3
Clarify what's meant by 'Suppress variant'
#129 opened Sep 14, 2023 by smsaladi
KeyError: 'SupportFraction' when running margin_cons.py
#128 opened Sep 14, 2023 by GammaCarbon7
Overlapping variants in fail.vcf and pass.vcf cause preconsensus to be masked and thus bcftools complains when applying the "pass" variant
#125 opened Mar 24, 2023 by Sam-Sims
2
no version information available (required by samtools)
#124 opened Mar 21, 2023 by alexahess
5
pipeline has stopped working...!
#121 opened Oct 18, 2022 by rebeelouise
4
Unable to install artic on mac
#116 opened Aug 9, 2022 by Rosina-Codes
vcf_filter.py filtering parameters and align_trim.py for alternative primer scheme
#114 opened Aug 2, 2022 by kakuk9
issue assigning variants occuring within an amplicon overlap region
#106 opened Feb 16, 2022 by george-githinji
3
Question: read group assignment in align_trim
#101 opened Jan 23, 2022 by gianfilippo
1
Medaka calls a 5 nt deletion instead of a 6 nt deletion
#100 opened Jan 19, 2022 by MarieLataretu
1
Question regarding align_trim.pl
#99 opened Jan 12, 2022 by ARastrojo
7
V1200/midnight primer scheme
#98 opened Dec 21, 2021 by rebeelouise
1
Deletion no longer being called
#97 opened Dec 9, 2021 by cpmorris82
Could not find primer scheme
#96 opened Nov 5, 2021 by amv33576
1
EPI2ME ARTIC failing for Midnight primers
#95 opened Oct 5, 2021 by MMitali13
1
Variant in amplicon overlapping region
#94 opened Sep 14, 2021 by hannahgoldswain
2
SNP filtering/masking/soft clipping with medaka
#92 opened Aug 29, 2021 by shimbalama
Error when running with too few reads/very low coverage
#91 opened Aug 23, 2021 by Coppini
3
How do deal with overlapping mutations in pass.vcf and fail.vcf?
#90 opened Aug 17, 2021 by rpetit3
quality Filter for pass.vcf
#89 opened Aug 17, 2021 by pratibha-kadam
artic-tools check_vcf Segmentation fault on empty VCF files
#88 opened Aug 9, 2021 by rdeborja
5
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