annotations of SV

[Bogdan Tanasa]

Dear Brent,

please would you let me know, could we use vcfanno for the annotations of SV (deletions, duplications, inversions, translocations) ?
thanks,

bogdan

[Brent Pedersen]

Yes, you can.
vcfanno will look at the END (or SVLEN) field to get the full extent
of the SV or CNV and you can also annotate the regions at each end
defined by the CIPOS and CIEND if you specify -ends.
https://github.com/brentp/vcfanno#-ends

hope that helps,
-Brent

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[Bogdan Tanasa]

Dear Brent,

thank you for the quick reply. At the end, we would glad to have a list of the following sets of genes :

-- fusions (if both breakpoints are in exons, introns, utrs)

-- truncations (if only one breakpoint is in exon, intron, utr; and the other breakpoint is in intergenic area)

-- the genes in the areas that are deleted, duplicated, inverted

could we get all these annotations, and if yes, we would only need to specify the --end ? thanks a lot,

-- bogdan

On Tue, Mar 28, 2017 at 5:18 PM, Brent Pedersen <bped...@gmail.com> wrote:

Yes, you can.
vcfanno will look at the END (or SVLEN) field to get the full extent
of the SV or CNV and you can also annotate the regions at each end
defined by the CIPOS and CIEND if you specify -ends.
https://github.com/brentp/vcfanno#-ends

hope that helps,
-Brent

On Tue, Mar 28, 2017 at 5:14 PM, Bogdan Tanasa <tan...@gmail.com> wrote:
> Dear Brent,
>
> please would you let me know, could we use vcfanno for the annotations of SV
> (deletions, duplications, inversions, translocations) ?
> thanks,
>
> bogdan

>
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[Brent Pedersen]

Well, it won't do all of that for you but if you annotated with a bed
or GTF file of genes and --ends, then you could use a [postannotation]
block with a lua functtion to indicate likely events of those
categories

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