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31 Open 42 Closed
31 Open 42 Closed
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Issues list

locateVariants failing on intronic variants
#87 opened Aug 9, 2024 by jayoung
1
predictCoding on empty ranges drops REFAA/VARAA, should be empty AAStringSet instead?
#86 opened Aug 6, 2024 by mschubert
expand() and non-standard rowRanges columns
#85 opened Jul 19, 2024 by jayoung
1
nonsense mutations from DBS across two codons misclassified as nonsynonymous?
#84 opened Jul 11, 2024 by ChristofferFlensburg
Incorrect annotation of exon/intron boundary deletion
#83 opened Jul 3, 2024 by mschubert
readVcf does not recognize my vcf file?
#82 opened May 15, 2024 by igrabski
5
locateVariants() and predictCoding() silently drop large INDELs
#81 opened Apr 25, 2024 by johnstonmj
5
readVcf doesn't handle quoted = in hapmap_exome_chr22.vcf.gz correctly
#80 opened Jan 2, 2024 by LTLA
8
Convert Number=A to Number=1 when creating an ExpandedVCF
#79 opened Jan 2, 2024 by LTLA
5
Faithfully recapitulate metadata via a round-trip through writeVcf + readVcf.
#78 opened Jan 2, 2024 by LTLA
4
readVcf(), VariantAnnotation and shiny compatibility
#77 opened Dec 8, 2023 by FunGeST
1
expand Error data is NULL
#72 opened Aug 13, 2023 by DarioS
readVcf is Slow if ScanVcfParam which Regions is Lengthy
#70 opened Mar 27, 2023 by DarioS
3
writeVcf Output Causes IGV Errors from htsjdk
#65 opened Sep 12, 2022 by DarioS
5
Populate INFO column with VariantAnnotation::writeVcf
#61 opened May 31, 2022 by Al-Murphy
4
locateVariants returns genes from both Forward and Reverse strands in PRECEDEID and FOLLOWID
#55 opened Feb 23, 2022 by amizeranschi
3
readVcfStack(param=ScanVcfParam()) doesn't work if "which=" is not specified.
#50 opened Oct 6, 2021 by Liubuntu
Can geno() obtain the reference depth and alternate allele separately?
#48 opened Sep 17, 2021 by lihe-s
1
predictcoding - multiple mutations at a codon are never evaluated additively
#46 opened Mar 8, 2021 by ojcharles
1
REFCODON not consistent with REF
#43 opened Nov 3, 2020 by onebeingmay
Subset Fails if Info and Geno Excluded
#40 opened May 4, 2020 by DarioS
Proposal: String representation/RleMatrix
#38 opened Feb 28, 2020 by jonocarroll
6
API to change output suffix to .gz enhancement
#35 opened Oct 31, 2019 by d-cameron
7
ScanVcfParam which Parameter Description Inconsistency
#34 opened Oct 22, 2019 by DarioS
2
Import Error for bcftools Compressed Files
#32 opened Aug 5, 2019 by DarioS
1
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