Obtaining Aa Position From Snpeff Output:

Question

[Angel]

Hey,

I used SnpEff 2.0.5 to obtain INDELS and SNPs. Now I want to find the AA position corresponding to the genomic coordiantes e.g. output line from SNpEff below

7 140442544 C A SNP Het 19.1 9 ENSG00000157764 BRAF protein_coding ENST00000479537 TRANSCRIPT: ENST00000479537

Thanks very much, Angel

Answer 1

[Bert Overduin]

I would expect that, like the Ensembl Variant Effect Predictor, snpEff gives you the amino acid if your variant is in the coding region of a transcript. However, the location you are referring to is, as far as I can see, in an intron, so there is no amino acid there ....

Answer 2

[Mahdi Sarmady]

Hi,

If you run snpEff to get vcf output, you would get the amino acid change and position where there's a protein coding mutation. The following is an example of what snpEff would add to the INFO field:

EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I300V|NOC2L|mRNA|CODING|NM_015658|NM_015658.ex.11)

I300V is the amino acid change from I to V at position 300 of NM_015658's product. This example was annotated using refSeq but it would be in the same format for Ensembl. Check out here for more details.

[justinfanyi]

How would you extract that field (1300V)only?

[SemiQuant]

Hi justinfanyai.

There two option I can think of here, you can either set SnpEff output to GATK and then grep for "SNPEFF_AMINO_ACID_CHANGE=" as this is how it is annotated with this option. The second, and method I use, is utilising the partner program SnpSift. This is very easy to use and you can find the manual here.