how to identify amino acids using snpEFF

Question

[zion22]

hi, thanks for reading this, I have a doubt, I am identifying snp using snpEFF with the following command:

snpEff eff -c snpEff.config my_genome -s output_.html -v "variants/imput_.vcf.gz" > "variants/output_.vcf.gz"

but I would also like to obtain the amino acid changes that were made, since the output.vcf only indicates the base change but not the amino acid.

thanks a lot

[Pierre Lindenbaum]

indicates the base change but not the amino acid.

not for me

$ gunzip -c rotavirus_rf.ann.vcf.gz  | cut -f 8 | tr ";" "\n" | grep ANN= | tr "," "\n" | sed 's/ANN=//' | grep misse | tr "|" "\t" | cut -f1-3,10-15 | column -t 
C  missense_variant  MODERATE  c.952A>C   p.Lys318Gln  952/3267   952/3267   318/1088
A  missense_variant  MODERATE  c.562G>A   p.Val188Ile  562/2643   562/2643   188/880
A  missense_variant  MODERATE  c.861T>A   p.Asn287Lys  861/2643   861/2643   287/880
G  missense_variant  MODERATE  c.1171C>G  p.Leu391Val  1171/2508  1171/2508  391/835
A  missense_variant  MODERATE  c.1192C>A  p.Leu398Ile  1192/2508  1192/2508  398/835
G  missense_variant  MODERATE  c.1638T>G  p.Asn546Lys  1638/2508  1638/2508  546/835
T  missense_variant  MODERATE  c.1658G>T  p.Gly553Val  1658/2508  1658/2508  553/835
A  missense_variant  MODERATE  c.2100T>A  p.Phe700Leu  2100/2508  2100/2508  700/835
G  missense_variant  MODERATE  c.878A>G   p.Glu293Gly  878/2331   878/2331   293/776
C  missense_variant  MODERATE  c.982T>C   p.Tyr328His  982/2331   982/2331   328/776
C  missense_variant  MODERATE  c.1891A>C  p.Met631Leu  1891/2331  1891/2331  631/776
T  missense_variant  MODERATE  c.467A>T   p.Asn156Ile  467/1476   467/1476   156/491
C  missense_variant  MODERATE  c.763A>C   p.Asn255His  763/1476   763/1476   255/491
G  missense_variant  MODERATE  c.1265T>G  p.Val422Gly  1265/1476  1265/1476  422/491
C  missense_variant  MODERATE  c.1307A>C  p.Gly436Ala  1307/1476  1307/1476  436/491
A  missense_variant  MODERATE  c.494C>A   p.Thr165Lys  494/1194   494/1194   165/397
C  missense_variant  MODERATE  c.520G>C   p.Asp174His  520/1194   520/1194   174/397
T  missense_variant  MODERATE  c.73G>T    p.Ala25Ser   73/942     73/942     25/313
A  missense_variant  MODERATE  c.200C>A   p.Ala67Glu   200/942    200/942    67/313
G  missense_variant  MODERATE  c.659T>G   p.Ile220Ser  659/942    659/942    220/313
C  missense_variant  MODERATE  c.880A>C   p.Lys294Gln  880/954    880/954    294/317
C  missense_variant  MODERATE  c.946G>C   p.Gly316Arg  946/954    946/954    316/317
G  missense_variant  MODERATE  c.5A>G     p.Glu2Gly    5/528      5/528      2/175
A  missense_variant  MODERATE  c.98T>A    p.Phe33Tyr   98/528     98/528     33/175
G  missense_variant  MODERATE  c.134C>G   p.Thr45Arg   134/528    134/528    45/175

Answer 1

[Rob]

When the mutation is outside a coding region snpEff will not give you the potential amino acid change because there is no amino acid. If you look in coding region you will find amino acid modification:

c.10G>A (It mean that in the 10th amino acid of this protein the G became an A)