Predict Impacts of variants (from VCF file) using Dog Models

Question

[sruthimouli88]

Hello,

I am using Dog Genome as a model of my study. I wish to annotate my VCF files with Polyphen2 . The tool describes that the input has to be formatted in a specific way for running the tool for a non-human model. It is also mentioned that tools like snpEff can be used. My vcf files are annotated with snpEFF. But I do bot have all the required fields.

This is an example of my annotated VCF file I have. I am not sure if this is sufficient.

chr1    1105    .    C    A       .  AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;DP=14;DP4=2,5,1,1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R129L|Q56JJ8_CANFA_4|stdin||Q56JJ8_CANFA_4|3)

Can someone help me with how to proceed formatting my annotated vcf file to give as an input to PolyPhen2

Thanks,
Sruthi