annotating a vcf file containing Structural Variants
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
1 answer
ANNOVAR is my personal choice for annotating various genomic regions.
Some more options:
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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