annotating a vcf file containing Structural Variants

Question

[Bogdan]

Dear all,

a simple question emerging from the SV calling efforts at their very beginning :

what tools would you recommend to use in order to annotate the VCF files (containing DEl, DUP, INV, TRA, INS) with the gene information (or other genome information) ?

thanks !

-- bogdan

[LGMgeo]

SV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information) can be easily automated !

You can look at this post describing the annotSV tool: Annotation for SV and CNV

Answer 1

[igor]

ANNOVAR is my personal choice for annotating various genomic regions.

Some more options:

• How Can I Annotate Cnvs
• What Is The Best Tool For Mouse (Mm9 Or Mm10) Variant Annotations?

[Bogdan]

thank you, Igor ! I was just not very sure how Annovar works on the vcf formats from DELLY and MANTA ;)

[igor]

It should work on any VCF. You can also convert VCF to ANNOVAR format with convert2annovar.pl and see if the output looks reasonable.

[Bogdan]

yes, indeed, Annovar works if I have the file in the format :

chr start end 0 0 chr start end 0 0