Bioconductor/VariantAnnotation

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Annotation of Genetic Variants

Stars: 32
Forks: 21
Open beginner issues: 0
Indexed issues: 33

Dominant language: R
License: No license data
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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33 open issues indexed

refactor the package Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/VariantAnnotation#115 · 4 comments · Opened Jul 7, 2026
what is the "covr" condition of this package? Open

Bioconductor/VariantAnnotation#114 · 1 reaction · 2 assignees · Opened Jul 7, 2026
produce false positive and false negative PRs Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

Bioconductor/VariantAnnotation#113 · 2 comments · Opened Jul 7, 2026
possible problem parsing INFO description field Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#89 · Opened May 22, 2025
ensemblVEP::parseCSQToGRanges Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

Bioconductor/VariantAnnotation#88 · 2 comments · Opened Mar 7, 2025
locateVariants failing on intronic variants Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

Bioconductor/VariantAnnotation#87 · 1 comment · Opened Aug 9, 2024
`expand()` and non-standard rowRanges columns Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Bioconductor/VariantAnnotation#85 · 1 comment · Opened Jul 19, 2024
nonsense mutations from DBS across two codons misclassified as nonsynonymous? Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

Bioconductor/VariantAnnotation#84 · Opened Jul 11, 2024
Incorrect annotation of exon/intron boundary deletion Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#83 · Opened Jul 3, 2024
readVcf does not recognize my vcf file? Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Bioconductor/VariantAnnotation#82 · 6 comments · Opened May 15, 2024
locateVariants() and predictCoding() silently drop large INDELs Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#81 · 5 comments · Opened Apr 25, 2024
`readVcf` doesn't handle quoted `=` in `hapmap_exome_chr22.vcf.gz` correctly Open

Difficulty 3/5 1-2 days Newbie friendliness 62/100

Bioconductor/VariantAnnotation#80 · 10 comments · Opened Jan 2, 2024
Convert `Number=A` to `Number=1` when creating an `ExpandedVCF` Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

Bioconductor/VariantAnnotation#79 · 5 comments · Opened Jan 2, 2024
Faithfully recapitulate metadata via a round-trip through `writeVcf` + `readVcf`. Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

Bioconductor/VariantAnnotation#78 · 5 comments · Opened Jan 2, 2024
readVcf(), VariantAnnotation and shiny compatibility Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Bioconductor/VariantAnnotation#77 · 1 comment · Opened Dec 8, 2023
expand Error data is NULL Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#72 · Opened Aug 13, 2023
readVcf is Slow if ScanVcfParam which Regions is Lengthy Open

Difficulty 4/5 3-5 days Newbie friendliness 43/100

Bioconductor/VariantAnnotation#70 · 4 comments · Opened Mar 27, 2023
writeVcf Output Causes IGV Errors from htsjdk Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

Bioconductor/VariantAnnotation#65 · 5 comments · Opened Sep 12, 2022
Populate INFO column with VariantAnnotation::writeVcf Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#61 · 4 comments · Opened May 31, 2022
locateVariants returns genes from both Forward and Reverse strands in PRECEDEID and FOLLOWID Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Bioconductor/VariantAnnotation#55 · 3 comments · Opened Feb 23, 2022
readVcfStack(param=ScanVcfParam()) doesn't work if "which=" is not specified. Open

Difficulty 3/5 1-2 days Newbie friendliness 57/100

Bioconductor/VariantAnnotation#50 · 1 comment · Opened Oct 6, 2021
Can geno() obtain the reference depth and alternate allele separately? Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

Bioconductor/VariantAnnotation#48 · 1 comment · Opened Sep 17, 2021
predictcoding - multiple mutations at a codon are never evaluated additively Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#46 · 1 comment · Opened Mar 8, 2021
REFCODON not consistent with REF Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#43 · 1 comment · Opened Nov 3, 2020
Proposal: String representation/RleMatrix Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/VariantAnnotation#38 · 6 comments · Opened Feb 28, 2020
API to change output suffix to .gz Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Bioconductor/VariantAnnotation#35 · 7 comments · 3 reactions · Opened Oct 31, 2019
ScanVcfParam which Parameter Description Inconsistency Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

Bioconductor/VariantAnnotation#34 · 2 comments · Opened Oct 22, 2019
Import Error for bcftools Compressed Files Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#32 · 1 comment · 7 reactions · Opened Aug 5, 2019
Ambiguous Description of Ellipsis for readVcf Open

Difficulty 2/5 1-3 hours Newbie friendliness 40/100

Bioconductor/VariantAnnotation#31 · Opened Aug 1, 2019
Can I read in a VCF "file" as a character string? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Bioconductor/VariantAnnotation#28 · 1 comment · Opened Apr 15, 2019
Create protein sequences including variants from a VCF file Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/VariantAnnotation#24 · 3 comments · Opened Mar 8, 2019
Filtering VCF by ranges Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/VariantAnnotation#5 · Opened Feb 14, 2018
merging VCF objects Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Bioconductor/VariantAnnotation#3 · 9 comments · 2 reactions · Opened Jan 23, 2018

Bioconductor/VariantAnnotation

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