Question: annotating a vcf file containing Structural Variants
0
gravatar for Bogdan
2.6 years ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

Dear all,

would welcome any suggestion regarding a  package I could use for annotating the structural variants (especially duplications, inversions, translocations). Many thanks,

 

-- bogdan

 

 

vcf • 515 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Bogdan550

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

ADD REPLYlink written 2.6 years ago by Valerie Obenchain6.7k
Answer: annotating a vcf file containing Structural Variants
0
gravatar for Bogdan
2.6 years ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

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

 

 

ADD COMMENTlink written 2.6 years ago by Bogdan550

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

 

ADD REPLYlink written 2.6 years ago by Valerie Obenchain6.7k

Thanks Valerie !

ADD REPLYlink written 2.6 years ago by Bogdan550
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