Question: Predict Impacts of variants (from VCF file) using Dog Models
0
gravatar for sruthimouli88
4.4 years ago by
Finland
sruthimouli8820 wrote:

 

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

 

 

ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 4.4 years ago by sruthimouli8820
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: 919 users visited in the last hour