Annotation of vcf with snpEff

Question

[Peerzada]

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

Answer 1

[Pierre Lindenbaum]

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.

[Peerzada]

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.

[Pierre Lindenbaum]

define

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

what do you need for your output ?

[Peerzada]

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 .

[Pierre Lindenbaum]

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

[Peerzada]

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 .

[Peerzada]

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 .