several effect for one SNP annotated by SNPeff

Question

[reza]

hi

i annotated one vcf file using SNPeff and now some SNPs have several effect instead one effect, for example:

ANN=A|splice_acceptor_variant&splice_donor_variant&intron_variant|HIGH|LOC105079267|gene19881|transcript|rna26374|protein_coding|4/6|c.2134+1C

effect of splice_acceptor_variant and splice_donor_variant is high, while effect of intron_variant is modifier. what is problem? anyone can help me?

Answer 1

[Kevin Blighe]

See these:

These are the transcript splice isoforms of BRCA1, taken from UCSC Genome Browser. Different exons are transcribed in different isoforms.

When we describe a genetic variant using the standard nomenclature, we only provide chromosome, base position, ref allele, and alt allele. The only way that we can comprehensively annotate variants using this simple information is by annotating it for all known splice isoforms for the gene in which the variant is located.

Looking at the screenshot that I provide, you can appreciate that there are many regions in this gene where the variant would be in an exon and intron, depending on the splice isoform.

Additionally, in the human genome, there are many regions where 2 independent genes share overlapping sequence. In these cases, we have to annotate the variant for both genes, and their splice isoforms (if applicable).

Kevin

[Vitis]

SnpEff accepts custom annotations from GFF3 files. See this:

Building Snpeff Database

[reza]

i did it, i described it in my question

[Vitis]

I mean, you could probably create a simplified annotation in GFF3 format and make another SnpEff database. In the simplified version, you may only allow one transcript for one gene (based on expression profiles?), although I would not recommend it.

[reza]

thanks Kevin

ANNOVAR can help me i guess. i have reference (fasta) file and gff3 file of under study organism. i read ANNOVAR manual for annotation of vcf file by gff3 file but it puzzled me because all the examples are about a human that has all kind of required data. can you help me to do that? anyone here work with ANNOVAR?

[Kevin Blighe]

Why do you not have a VCF? Have you called variants from your FASTA reads? Have you even aligned the FASTA reads to the reference genome? Which species is it?

[reza]

i have vcf file resulted from standard workflow of variant calling (fastq files mapped to reference genome, post-alignment steps, variant calling by samtools). under study species is Bactrian camel

[Kevin Blighe]

Indeed, ANNOVAR will not have annotation for the Bactrian camel.