Software to annotate variants

[binfoUser]

I am wondering if there is any software that annotates variants not by the variants genomic coordinates but by their position in the cDNA.

Thank you

[HESmith]

If you use the transcriptome for your reference instead of the genome, then yes.

[binfoUser]

Do you mean the reference used to find the variants in the sequence? Or the reference used by the annotation software?

[HESmith]

Both: the alignment and annotation references have to match. But your original question implied that you had already determined variant positions by cDNA coordinates. Was that not correct?

If your intended question was "how do I determine the positions of variants in cDNAs?", that's standard output for most variant annotating software. The genome is reference, and gene annotation tables (refGene or GFF3) are used to identify those variants contained within coding sequences.

[binfoUser]

But I only have the file with the variants already identified, nothing else. And due to the nomenclature, some variants can't be annotated by their genomic coordinates.

[HESmith]

How were your variants identified (i.e., what was the software pipeline)? And what format are they in? (posting ~10 lines would be useful)

[binfoUser]

I don't know the pipeline used to identify the variants. The only thing that I have access to is the reference file used, that was: hg38.fa
The variants are saved in a VCF file. What I want to do is to annotate the variants, but some variants do not match the genomic coordinate (when the variants involve more than one nucleotide), and in that case using a software that annotates by genomic coordinate will not perform a correct annotation.

[HESmith]

If hg38 was the reference used for alignment and variant calling, then the variants in your VCF have genomic (not cDNA) coordinates. Is that not true? And most variant annotation software can accommodate multi-nucleotide variants, so your question/concern is unclear.

Please post an example of a variant from your VCF with more than one nucleotide.

[GenoMax]

but some variants do not match the genomic coordinate (when the variants involve more than one nucleotide)

Then you may have a problem. You should go back and ask for whoever did the analysis for you for the reference they used.