[Bioc-devel] strandless introns with VariantAnnotation::locateVariants()

[Valerie Obenchain]

Thanks for the report.

Now fixed in release (1.14.2) and devel (1.3.25).

Valerie



On 06/09/2015 09:44 AM, Robert Castelo wrote:
> hi,
>
> currently, the annotation of variants in intronic regions by
> VariantAnnotation and the locateVariants() function does not assign
> strand to annotations in introns:
>
> library(VariantAnnotation)
> example(locateVariants)
> loc_all[loc_all$LOCATION == "intron"]
> GRanges object with 2 ranges and 9 metadata columns:
>     seqnames         ranges strand | LOCATION  LOCSTART    LOCEND
> QUERYID        TXID         CDSID      GENEID
>        <Rle>      <IRanges>  <Rle> | <factor> <integer> <integer>
> <integer> <character> <IntegerList> <character>
>         chr1 [13302, 13302]      * |   intron       948       948
> 3           2                 100287102
>         chr1 [13327, 13327]      * |   intron       973       973
> 4           2                 100287102
>           PRECEDEID        FOLLOWID
>     <CharacterList> <CharacterList>
>
>
>    -------
>    seqinfo: 1 sequence from hg19 genome; no seqlengths
>
>
> however, introns are stranded, so I would suggest to include the strand
> information in variants annotated to intronic regions. After a quick
> look to the source code I believe the relevant line is within the
> private function .makeResult(), concretely at:
>
>                  strand=strand(query)[xHits],
>
> where is taking the strand of the query (the variant) while I guess it
> should be the subject (the annotation).
>
>
> cheers,
>
> robert.
>
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