Understanding Annovar Output

Question

[newbinf]

I have a vcf output from Annovar (and wAnnovar), and need some help understanding all of the headers. I know i am given the reference and the alternative allele. However, I want to know how many reads in my input file were reference and alternative.

I'm looking at the vcf file, and see some trailing information. What do these mean? Do these value tell me how many reads per allele?

ADP=5;WT=0;HET=1;HOM=0;NC=0

GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:6:5:5:3:2:40%:2.2222E-1:75:48:3:0:2:0

Answer 1

[h.mon]

There is an ANNOVAR intro here:

Introduction to VCF file and some of its complications

And you can get a description of each attribute from the VCF headers, see this Pierre Lindenbaum answer.

The VCF specification is quite lengthy, and you have to read it if you want to understand VCF files in depth. However, as VCF files are a bit complicated there is plenty of discussions around, for example here at BioStars:

Regarding vcf output

VCF format: what does AD 1,0 denote?

Vcf files fields: AD vs DP4

Answer 2

[newbinf]

I realize that DP:RD:AD is total reads: reference allele reads: alternative allele reads. Please correct me if I am wrong.

How do I isolate these values. Or are there columns in the VCF file output that contain these values already?