locateVariants() and predictCoding() silently drop large INDELs

[johnstonmj]

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

This represents a deletion of 2542 bp.

The large deletion is present when I call
rowRanges(vcf)

So it is successfully being read by readVcf()

However, when I call:

locateVariants(
  vcf,
  txdb,
  AllVariants(
    promoter = PromoterVariants(0,0),
    intergenic = IntergenicVariants(0,0)
    )
  )

or
predictCoding(vcf, txdb, seqSource=fasta)

this variant position is not included among the results.

With some trial and error, I have determined that truncating the REF sequence to 800 characters allows the variant to be maintained, but 850 characters fails.

Success, 850 bp
contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTG 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

Fails, 900 bp
contig_xyz 133527 Sniffles2.DEL.50S0 GGATGAACTCTTGGATTCTTGGGCTCATGTCGGACAGGATGCCGCCCCAGCTTCTCAGGTTGATGCCCTGGGATCTAGAATCCAGCAGTGTGGGCAGCACCCGGAACAGCTTGAAGAAGTCCACGTTGGCGTACAGGGTATCCTCGATCCACTGCAGGGTTCCCTGGCTCAGACTGCACAGGGCATATCTGACGGTCTTGGCGCCTCTCCGCTGGCTGAAGATGATGAACCGTTCCAGCAGGGCCTCAGAACAGGCGATATCCTTCAGGGCGAGATCTGGCACGCCATGAGCAAACTGCTCGGGCCGCACTTGGCTGTTGATCAGCAGGTACACCACGCTGTCGCTCAGGCCGATGTTCTTGATGAGGAACAGTGTCAGGGTTTCCTCGTCCTTCAGGATGTCCCGGATTCTGATGCCCCTGCCGGCGATTCTCTCGGGGTGTGTTCTCAGGGTGTCCATGAACTGGCTCAGGATGTGCAGCTCGGTCCAGATTCTGCCCAGGTGCTGAGACTCAGGGGCGTTCATCAGCAGCTCTTGGAAGTCCCGGTACACTCTGGCCAGGATGCTGTTGTTGTAGTTGGACACGATGCCAGGGCTTTCGCCAGGTGTGGGGCTCTGAAAGCAGGGGTTGTTCACGTTGCAGAAGATGCCCTGCAGCCAAGGCAGCATTCCGGCAGAAGGCATGGCCTTGTTGGGGAAGTGACACTCGTGGTGGCTGTACAGAGGATTGGCGTTCCGCAGCCAGATCAGCACCAGAAACAGGCTCAGGGGCCACACGAGTTCCACCACGAATCTGATTTTCTGCCGCTTCCGCAGGGTCCAGTTCTTCCACAGCAGCAGCTGAATCTGCCGCACGAATCCCATGGTGGCCAGCTCGGTCGTCCCGGGGCCTCTACTGT 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

Can you suggest a way to maintain these large INDELs among the results?
Alternatively, if it is impossible to maintain large INDELs, could a warning or error be returned instead of a silent discard?

Thanks!

[vjcitn]

Thanks very much for this report. Would you be willing to share the VCF or a slice of it that is sufficient to reproduce the problem?

[johnstonmj]

I've attached a minimal example here.
min_example.zip

Also, sessionInfo()

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_American Samoa.utf8  LC_CTYPE=English_American Samoa.utf8   
[3] LC_MONETARY=English_American Samoa.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_American Samoa.utf8    

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VariantAnnotation_1.48.1    Rsamtools_2.18.0           
 [3] Biostrings_2.70.3           XVector_0.42.0             
 [5] SummarizedExperiment_1.32.0 Biobase_2.62.0             
 [7] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        
 [9] IRanges_2.36.0              S4Vectors_0.40.2           
[11] MatrixGenerics_1.14.0       matrixStats_1.2.0          
[13] BiocGenerics_0.48.1         dplyr_1.1.4                

[vjcitn]

Wonderful example. I think the problem you are observing arises from

setMethod("mapToTranscripts", c("GenomicRanges", "GRangesList"),
    function(x, transcripts, ignore.strand=FALSE, intronJunctions=FALSE)

in GenomicFeatures, where there is an overlap test that uses type "within".

The initial developers of both GenomicFeatures and VariantAnnotation are long
departed from the project. I think we may have to promote overlap type setting
to a parameter but we'll have to discuss internally. @hpages

[johnstonmj]

Ah, so it might be because the deletion extends beyond the end of a single annotated feature?
Or potentially extends into the next annotation?
That would make sense.
Thanks for investigating!

[vjcitn]

OK -- so what are your thoughts? Would you want to make a PR that identifies the event and emits message or warning, or is the behavior reasonable in this form? We could just improve the documentation.