Where to find info on VCF file format?

Question

[_quantum_girl_]

The format of my vcf file is:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr8 1023470 chr8_1023470_T_G T G 48 . AF=3e-06;AQ=48 GT:DP:AD:GQ:PL:RNC

What do AQ, AD and RNC mean?

I tried looking here: https://samtools.github.io/hts-specs/VCFv4.1.pdf but couldn't find them.

[Ram]

You need to read manuals carefully before asking questions here. It's literally right there in the link in your post: https://samtools.github.io/hts-specs/VCFv4.1.pdf#subsubsection.1.2.4

Answer 1

[Shred]

Fields are declared on top of the VCF, with commented lines (starting with ##)

Answer 2

[Ram]

Adding on to Shred's answer, VCF is flexible and self-describing so you won't find the meaning of all fields in your VCF in the file specification. See this part of the file spec (linked in your post):

It is strongly encouraged that information lines describing the INFO, FILTER and FORMAT entries used in the body of the VCF file be included in the meta-information section.

so go to the meta-information section. What's that, you ask?

File meta-information is included after the ## string and must be key=value pairs

So you're looking for FORMAT/AQ, FORMAT/AD and FORMAT/RNC. These translate to header (meta-information) lines that look like:

##FORMAT=<ID=AQ,....
##FORMAT=<ID=AD,....
##FORMAT=<ID=RNC,....

Look for those lines and you'll see what each of those fields means.