VCF INFO interpretation

Question

[Martina]

Hello guys, I am quite new in the processing of NGS data (exome) and I would like to understand all the INFO and FORMAT fields in VCF. I know that the description is in the header of VCF but for some fields like End Placement Probability, it is harder to understand it and sometimes even google it out. I am searching hard for some material where these terms would be properly defined, mathematical equations might be also great. Could you please recommend me something like this? Or at least some of papers where all that staff was defined? Or maybe some videos? Books? Anything that will come to your mind would be great. Thank you very much!!!! :)

Martina

[Martina]

Thank you very much! I still have several variables about which I am not 100% that I fully understand its meaning. I wanted to post here everything, but I don't have time to do it now, so at this moment I really appreciate your answers and I will post progress here later.

Bye for now :) Martina

Answer 1

[benformatics]

I believe all the information should be available in the VCF format specification document (click on the most recent VCF file on the left-hand column) - at least for all standard INFO fields.

It sounds like you might be using freebayes so maybe check out their pre-print.

You could also check out GATK's page on VCF files.

Here are some additional variant calling tutorials I found online:

1. https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day2/vcf-intro.nb.html
2. http://clavius.bc.edu/~erik/CSHL-advanced-sequencing/freebayes-tutorial.html

[John Marshall]

Your go-to link for VCF should be the 4.3 spec. The differences between 4.1/4.2/4.3 are fairly minor for people examining data in them, and lots of things common to all three are best described in the latest specification.