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