Annotation of vcf with snpEff
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2.2 years ago
Peerzada • 0

Hello Everyone,

I have a multi sample vcf file of a particular gene for 1000 individuals . I annotated it with snpeFF. I want to know that what amino acid and codon changes these variants are creating in each individuals . Also I want to know the position of amino acid change in the protein formed from these variants .In snpEff output summary file I am getting the overall codon and amino acid changes but I want to know the position of change and individual also. In short I want my annotation results be like that they show the position of amino acid and codon change in each individual by these variants . Kindly tell about some approach or tool for the same.

Thank you

vcf 1000 genome annotation • 1.5k views
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2.2 years ago

The VCF output of SnpEff already contains everything you want. https://pcingola.github.io/SnpEff/se_inputoutput/#ann-field-vcf-output-files

Allele (or ALT): In case of multiple ALT fields, this helps to identify which ALT we are referring to.

Protein_position / Protein_len: Position and number of AA (one based, including START, but not STOP).

you just to loop over each genotype to check if a sample has the ALT allele.

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As I am new to all this , Can you tell me how can I proceed further as I have output snpEff vcf.ann file for 1000 individuals and I am keen to get the variation in the protein from variants .I got your answer but I am not able to get the information present in the info column of annotation file .Basically I have variants of aqp1 gene in 1000 individuals and I have to find the variation in the protein that will be formed in each individual.

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define

I have to find the variation in the protein that will be formed in each individual.

what do you need for your output ?

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I need the protein sequence with the changed amino acid due to variants so that I can see where in the protein sequence we have the variation .

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that's still not clear. You already have the position of the new amino acid what do you need more to "see" where in the protein sequence we have the variation

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Actualy there are also the samples which do not contain variant and have the reference allele in homozygous form. I only need the samples with variation and the position of variation. How can I fIlter that from this data .

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I got the Warning that "WARNING_TRANSCRIPT_NO_START_CODON" and "INFO_REALIGN_3_PRIME" .That is why my results from snpeFF are not very clear.What is the probable issue in this .

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