ncbi / vadr

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

Repository from Github https://github.comncbi/vadr

ncbi/vadr Issues

bug: vadr annotation erroneous coordinates/matchs for avian coronavirus
Updated 10 months ago5
Model info file: alternative_ftr_set_subn values don't work properly if they contain whitespace
Updated a year ago
v-annotate.pl cannot be run with apptainer exec using the VADR Biocontainers Apptainer/Singularity image
Updated a year ago
Error in install from Inline module
Closed a year ago10
v-annotate.pl bug: cdsstopp alert causes script to fail if early stop position exceeds CDS model length
Closed a year ago2
Frameshifts for 5' truncated alignments beginning with an insert are mishandled
Closed a year ago1
Outdated MODEL-VERSIONS.txt previnting automated model download
Closed a year ago2
Installation Issue 1.5.1
Closed a year ago8
Unable to build a model(NC_006273)
Closed a year ago1
Bioconda - 1.6.3 broken symlink
Closed a year ago3
Bug: v-annotate.pl does not report cdsstopn for early in-frame stop codons in 3' truncated CDS if they are the final 3 nt of the input sequence
Closed 2 years ago3
Extra header lines in .vadr.sqa
Closed a year ago2
compatibility with `-` and `.` in input assemblies
Closed a year ago2
v-build.pl 1.6.3 fails on mac os/x
Closed a year ago1
conda/mamba installation improvement
Closed a year ago5
Installation Documentation: vadr-install.sh download link
Closed 2 years ago1
Problem with building a model library
Closed 2 years ago4
v-annotate.pl fails with 'unable to open file' error on mac os/x
Closed 2 years ago1
Bug: codon_start and truncation flag (<) missing in .tbl for multi-segment CDS if sequence begins after end of segment 1
Closed 2 years ago1
Bug: early stops misreported for multi-segment CDS
Closed 2 years ago1
Is there a database built for most viruses?
Closed 2 years ago2
Error: summed psi of split states in node 32146 not 1.0 but : 1.001000
Closed 2 years ago8
Problem about fetching and parsing protein feature table file(s)
Closed 2 years ago9
ERROR in utl_RunCommand() in vadr 1.5 installed via conda
Closed 3 years ago18
Incorrect reporting of short frameshifts in 5' truncated CDS in rare cases
Closed 3 years ago1
Bug in parse_blast.pl script causes max length deletion to be incorrectly reported in rare cases
Closed 3 years ago1
ERROR in sqf_EslTranslateCdsToFastaFile, problem translating CDS feature, unable to find expected translated sequence in EU156171/EU156171.vadr.cds.esl-translate.2.fa:
Closed 3 years ago3
ERROR in vdr_EutilsFetchToFile, problem fetching NC_063383.1 (undefined)
Closed 3 years ago
Unable to build a model
Closed 3 years ago2
Bug: parse_blast.pl incorrectly detects strand if alignment line length is 1
Closed 3 years ago1
problem with git clone corona on bitbucket
Closed 3 years ago2
cdsstopp can be reported for stop codon that overlaps with replaced region (due to -r)
Closed 4 years ago1
VADR exits due to limited memory, but doesn't report this to the user
Closed 4 years ago5
VADR doesn't detect annotated segments
Closed 4 years ago4
Error in v-build.pl on example command
Closed 4 years ago2
VADR produces qualifier with invalid value
Updated 4 years ago4
VADR predicted nested genes, prevents submission to ENA
Updated 4 years ago4
VADR doesn't annotate second segment of segmented CoV genome
Updated 4 years ago6
Understanding `misc_feature` with no qualifiers
Closed 4 years ago4
Double-entries in `.tbl` file
Closed 4 years ago2
To generate GenBank format of a complete genome of SARS-CoV2 variants
Closed 4 years ago2
`ERROR in output_feature_table`
Closed 4 years ago3
Test failed when running `do-all-tests.sh` with VADR 1.3
Closed 4 years ago3
Documentation: vadr-map-model-coords.pl command in wiki
Closed 4 years ago1
Consider adding a script to download models
Closed 4 years ago2
Issue in installation - reg
Closed 4 years ago11
install issue： mv: cannot move ‘vadr-vadr-1.2’ to ‘vadr/vadr-vadr-1.2’: Directory not empty
Closed 4 years ago4
With -r, some N-rich regions not replace because overlapping blastn hits are thrown out
Closed 4 years ago1
Feature request: Separate install script into online and offline sections
Closed 4 years ago3
Problems in v-test.pl file
Closed 4 years ago5