Question: how to identify amino acids using snpEFF
3
gravatar for zion22
17 months ago by
zion2250
merilla
zion2250 wrote:

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

snp next-gen genome gene • 657 views
ADD COMMENTlink modified 17 months ago by Rob120 • written 17 months ago by zion2250
2

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
ADD REPLYlink written 17 months ago by Pierre Lindenbaum131k
2
gravatar for Rob
17 months ago by
Rob120
Rob120 wrote:

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)
ADD COMMENTlink written 17 months ago by Rob120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1506 users visited in the last hour