VariantAnnotation
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Bioconductor
Annotation of Genetic Variants
I have encountered an issue with large INDELs being silently discarded from my results. This is the offending VCF entry: `contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTGCCGCACGAATCCCATGGTGGCCAGCTCGGTCGTCCCGGGGCCTCTACTGTCCAGAGTCCTCCGCGGATCCCGATCTGACGGTTCACTAAACGAGCTCTGTTTATATAGACCTCCCACCGTACACGCCTACCGCCCATTTGCGTCAACGGGGCGGGCGATCGCAGTTGTTACGACATTTTGGAAAGTCCCGTTGATTTTGGTGCCAAAACAAACTCCCATTGACGTCAATGGGGTGGAGACTTGGAAATCCCCGTGAGTCAAACCGCTATCCACGCCCATTGGTGTACTGCCAAAACCGCATCACCATGGTAATAGCGATGACTAATACGTAGATGTACTGCCAAGTAGGAAAGTCCCGTAAGGTCATGTACTGGGCATAATGCCAGGCGGGCCATTTACCGTCATTGACGTCAATAGGGGGCGGACTTGGCATATGATACACTTGATGTACTGCCAAGTGGGCAGTTTACCGTAAATACTCCACCCATTGACGTCAATGGAAAGTCCCTATTGGCGTTACTATGGGAACATACGTCATTATTGACGTCAATGGGCGGGGGTCGTTGGGCGGTCAGCCAGGCGGGCCATTTACCGTAAGTTATGTAACGCGGAACTCCATATATGGGCTATGAACTAATGACCCCGTAATTGATTACTATTAATAACTAGTCAATAATCAATGCCAACATGGCGGTCATATTGGACATGAGCCAATATAAATGTACATATTATGATATAGATACAACGTATGCAATGGCCAATAGCCAATATTGATTTATGCTATATAACCAATGAATAATATGGCTAATGGCCAATATTGAAGATCCCCGGGTACCGAGCTCGAATTCATCGATGATGATCCACTAGTAACGGCCGCCAGTGTGCTGGAATTCGCCCTTCCCGCATGGCATCTCATTACCGCCCGATCCGGCGGTTTCCGCTTCCGTTCCGCATGCTAACGAGGAACGGGCAGGGGGCGGGGCCCGGGCCCCGACTTCCCGGTTCGGCGGTAATGTGATACGAGCCCCGCGCGCCCGTTGGCCGTCCCCGGGCCCCCGGTCCCGCCCGCCGGACGCCGGGACCAACGGGACGGCGGGCGGCCCTTGGGCCGCCCGCCTTGCCGCCCCCCCATTGGCCGGCGGGCGGGACCGCCCCAAGGGGGCGGGGCCGCCGGGTAAAAGAAGTGAGAACGCGAAGCGTTCGCACTTCGTCCCAATATATATATATTATTAGGGCGAAGTGCGAGCACTGGCGCCGTGCCCGACTCCGCGCCGGCCCCGGGGGCGGACCCGGGCGGCGGGGGGCGGGTCTCTCCGGCGCACATAAAGGCCCGGCGCGACCGACGCCCGCAGACGGCGCCGGCCACGAACGACGGGAGCGGCTGCGGAGCACGCGGACCGGGAGCGGGAGTCGCAGAGGGCCGTCGGAGCGGACGGCGTCGGCATCGCGACGCCCCGGCTCGGGATCGGGATCGCATCGGAAAGGGACACGCGGACGCGGGGGGGAAAGACCCGCCCACCCCACCCACGAAACACAGGGGACGCACCCCGGGGGCCTCCGACGACAGAAACCCACCGGTCCGCCTTTTTTGCACGGGTAAGCACCTTGGGTGGGCGGAGGAGGGGGGACGCGGGGGCGGAGGAGGGGGGACGCGGGGGCCGGAGGAGGGGGGACGCGGGGGCGGAGGAGGGGG G 59 PASS PRECISE;SVTYPE=DEL;SVLEN=-2542;END=136069;SUPPORT=259;COVERAGE=335,326,308,260,257;STRAND=+-;AF=0.869;STDEV_LEN=0;STDEV_POS=0 GT:GQ:DR:DV 1/1:60:39:259`...
It seems reasonable that per-allele `##INFO` fields should be converted from `Number=A` to `Number=1` when `expand()` is called, given that the 1:many relationship between rows and allelic values is now...
The header line for `GATKCommandLine` causes problems: ``` ##GATKCommandLine= ``` Calling `readVcf` gives me: ```r fl
`writeVcf` performs some unnecessary work that interferes with a perfect roundtrip of a `VCF` to a file and back. At the very least, these discrepancies interfere with my unit tests...
VCF files that are filtered using bcftools and have their data compressed by specifying `-O z` as part of the command can't be imported into R because of the error...
Hi, We are working on incorporating the readVcf function into our Shiny app, but it appears that Shiny is having trouble recognizing the object format. After completing the upload, we...
Thank for for the _VariantAnnotation_ package, it makes it very easy to annotate mutations found in VCF files! There is, however, one limitation that I find unnecessarily restrictive: The `predictCoding`...
It doesn't happen with the package's example file but does with [Genome Analysis ToolKit's gnomAD allele frequency file](https://www.bcgsc.ca/downloads/morinlab/reference/af-only-gnomad.hg38.vcf.gz). ```r populationFreq traceback() 6: array(vec, c(idxlen, xcols, 2L)) 5: .expandAD(gvarR, length(idx), ncol(x))...
Recently, U.S. Food and Drug Administration, National Institute of Standards and Technology and Illumina [researchers defined highly reproducible regions (H.R.R.s)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02569-8) of the human genome and [made available BED files](https://zenodo.org/record/5275189#.ZCDkyMpBzIX) to...
I created a subset file with seven samples out of two thousand and saved it to disk. IGV won't open it. > htsjdk.tribble.TribbleException: The provided VCF file is malformed at...