Where can I find Annotation info for VCF files?

Question

[akshaykum684]

Hello Everyone,

I have a VCF data with me and would like to do GWAS analysis as shown in tutorial here

May I know where can I find these annotation files?

I see that Annotation file contains info on Sex etc.

Where can I find these files and what is the use of these files?

I see that the column in this files are used as a additional columns to VCF files.

Can help me with this please?

[akshaykum684]

removed the post

Answer 1

[JC]

The "annotation" in external to the VCF file, so you need to check if you can get more information for the subjects in the VCF

[akshaykum684]

@JC - Thanks for the response. Upvoted. May I also check with you on the below

q1) How can a publicly available annotation file/database be used to get more information about my subjects (which are present in our VCF file). What fields are used to link between my source VCF file and the external annotation file?

q2) Should I interpret the link field in the VCF file (may I know what is that field?) is like a word (in a sentence) and the annotation file is like a dictionary (where we can find more information/meaning to the link field?)

q3) Is there any tutorial that explains the what, why and how behind VCF annotation for non-bioinformatics person like me?

[JC]

The VCF format only contains a header column which indicates Subject_ID, many public datasets has the information linking the IDs with the rest of the metadata in a separate file or somewhere. For example, in the 1000 Genomes project, the metadata is part of the file name and the data portal allows you to export more information per subject as a table

[akshaykum684]

@JC - Now, I have a set of VCF files with me and would like to annotate them. May I know how can it be done?

[JC]

If you mean to add Sex and Ethnicity for the 1000 Genomes, you can use this https://www.internationalgenome.org/data

[akshaykum684]