annotate VCF file with LRG ?

Question

[Richard]

Hi all,

We have recently been asked to try and annotate some vcf files with the LRG annotations

Are there any tools out there that anyone has used for the direct annotation of VCF files with the LRG annotations?

I didn't see any mention of it in snpEFF, and it is listed as something that might be doable with Ensembl's Variant Effect Predictor, but it looks like it could be tricky, so I'd like to hear if anyone has tried it before going down that road.

Answer 1

[Ashutosh Pandey]

You can create an annotation database in SnpEff. For this you will have to download the LRG data in a BED or some other standard format and convert it into BED format. Then you can use snpEff to annotate your vcf file.

Answer 2

[ning]

The LRG site now lists several tools that can perform this conversion, most of which are simpler, I think, than creating your own annotation database in SnpEff (though I think that may have been the norm 7 years ago). Some links I copied from the aforementioned list:

• NCBI Genome Remapping Service
• ENSEMBL Variant Recoder
• Mutalyzer 2's Position Converter