Bioconductor VariantAnnotation issues

Bioconductor / VariantAnnotation

Annotation of Genetic Variants

https://bioconductor.org/packages/VariantAnnotation

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issues

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locateVariants failing on intronic variants

#87 jayoung opened 3 months ago
1
`predictCoding` on empty ranges drops `REFAA`/`VARAA`, should be empty `AAStringSet` instead?

#86 mschubert opened 3 months ago
0
`expand()` and non-standard rowRanges columns

#85 jayoung opened 4 months ago
1
nonsense mutations from DBS across two codons misclassified as nonsynonymous?

#84 ChristofferFlensburg opened 4 months ago
0
Incorrect annotation of exon/intron boundary deletion

#83 mschubert opened 4 months ago
0
readVcf does not recognize my vcf file?

#82 igrabski opened 6 months ago
5
locateVariants() and predictCoding() silently drop large INDELs

#81 johnstonmj opened 6 months ago
5
`readVcf` doesn't handle quoted `=` in `hapmap_exome_chr22.vcf.gz` correctly

#80 LTLA opened 10 months ago
8
Convert `Number=A` to `Number=1` when creating an `ExpandedVCF`

#79 LTLA opened 10 months ago
5
Faithfully recapitulate metadata via a round-trip through `writeVcf` + `readVcf`.

#78 LTLA opened 10 months ago
4
readVcf(), VariantAnnotation and shiny compatibility

#77 FunGeST opened 11 months ago
1
locateVariant from VariantAnnotation returns wrong results

#76 nickhir closed 11 months ago
1
Memory Error for readGeno but not for readVcf

#75 grasshoffm closed 1 year ago
5
Allow 'ANY' txdb, eg. EnsDb objects

#74 mschubert opened 1 year ago
0
Add rworkflows

#73 bschilder closed 1 year ago
1
expand Error data is NULL

#72 DarioS opened 1 year ago
0
readVcf error: if (NROW(flesh) != flesh_len2) stop("shape of 'skeleton' is not compatible with 'NROW(flesh)'")

#71 jr1320 closed 1 year ago
6
readVcf is Slow if ScanVcfParam which Regions is Lengthy

#70 DarioS opened 1 year ago
3
Unable to load vcf file

#69 cyrusmallon closed 1 year ago
7
backward compatibility of info() function

#68 shwong-tw closed 1 year ago
12
Convert VariantAnnotation.Rnw, filterVcf.Rnw to VariantAnnotation.Rmd, filterVcf.Rmd

#67 villafup closed 1 year ago
2
Error message from predictCoding ()

#66 rwanwork closed 2 years ago
1
writeVcf Output Causes IGV Errors from htsjdk

#65 DarioS opened 2 years ago
5
data with AD field for demonstration of allele depth counting function ad_mats

#64 vjcitn closed 10 months ago
2
SNPlocs version in vignette needs updating

#63 jwokaty closed 2 years ago
1
predictCoding with incorrect predictions

#62 wshropshire closed 2 years ago
1
Populate INFO column with VariantAnnotation::writeVcf

#61 Al-Murphy opened 2 years ago
4
Write solo ##contig/##FILTER/etc lines as structured headers

#60 jmarshall closed 2 years ago
3
Speed up `readVcf`

#59 bschilder closed 2 years ago
16
Correct META API change version numbers to 1.27.5/.6

#58 jmarshall closed 2 years ago
0
Converting VCF --> data.table

#57 bschilder closed 2 years ago
18
Files do not exist error

#56 abalter closed 2 years ago
3
locateVariants returns genes from both Forward and Reverse strands in PRECEDEID and FOLLOWID

#55 amizeranschi opened 2 years ago
3
Different output on same command and same input file, different library version

#54 BCArg closed 2 years ago
3
predictCoding() and changes in start/stop codons?

#53 jayoung closed 2 years ago
5
`writeVcf` doesn't capture ALT Descriptions properly

#52 LTLA closed 2 years ago
4
Data Representation Efficiency of VCF

#51 DarioS closed 3 years ago
1
readVcfStack(param=ScanVcfParam()) doesn't work if "which=" is not specified.

#50 Liubuntu opened 3 years ago
0
readVcfStack(param=ScanVcfParam()) doesn't work if "which=

#49 Liubuntu closed 3 years ago
1
Can geno() obtain the reference depth and alternate allele separately?

#48 lihe-s opened 3 years ago
1
Add a covariate to VRange object

#47 xiw588 closed 3 years ago
4
predictcoding - multiple mutations at a codon are never evaluated additively

#46 ojcharles opened 3 years ago
1
Subset No Longer Works For Fixed Columns

#45 DarioS closed 3 years ago
1
Conversion to VRanges Error

#44 DarioS closed 4 years ago
2
REFCODON not consistent with REF

#43 onebeingmay opened 4 years ago
0
Incorrect added ##FILTER line when none are present.

#42 FreekManders closed 2 years ago
0
FILTER Replacement Causes Error

#41 DarioS closed 4 years ago
0
Subset Fails if Info and Geno Excluded

#40 DarioS opened 4 years ago
0
extractROWS() on a CollapsedVCF instance returns an invalid object.

#39 mtmorgan closed 4 years ago
5
Proposal: String representation/RleMatrix

#38 jonocarroll opened 4 years ago
6