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Dear all,
would welcome any suggestion regarding a package I could use for annotating the structural variants (especially duplications, inversions, translocations). Many thanks,
-- bogdan
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HI Valerie,
thank you for your reply. Talking about the structural variants, in principle, I would like to do the following :
-- for inversions, duplications, deletions (and insertions) : to know the genes that are affected by these chromosomal alterations (and if the chromosomal alteration impacts on exons, introns, or intergenic regions),
-- for translocations: to know the closest genes (or the closest exons) that are impacted by the translocation.
any suggestions are welcome. many thanks,
--~ bogdan
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With the genomic location of the variants, you can use VariantAnnotation::locateVariants() to get associated information out of a TxDb or any gene model you provide as a GRangesList. For example, from the ?locateVariants man page 'loc_all' is the GRanges output from a call to locateVariants(..., region=AllVariants()). It has the following metadata columns:
> names(mcols(loc_all))
[1] "LOCATION" "LOCSTART" "LOCEND" "QUERYID" "TXID" "CDSID"
[7] "GENEID" "PRECEDEID" "FOLLOWID"
This provides the gene the variant falls in (if any), the closest preceding and following genes, the transcript etc. Not sure if that helps you. Maybe others will jump in with their suggestions.
Valerie
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Can you be more specific about the type of data you have (e.g., have you already identified variant type?) and what annotations you're after?
Valerie