How to interpret snp frequency

Question

[Stane]

Hi, I am running VCFtools --freq on a vcf files that contains 17 individuals the output is :

CHROM   POS N_ALLELES   N_CHR   {FREQ}
1   13504   2   2   0.5 0.5
1   19776   2   2   0.5 0.5
1   19788   2   2   0.5 0.5
1   21580   2   6   0   1
1   22158   2   3   0   1
1   23975   2   13  0   1
1   30860   2   1   0   1
1   35510   2   2   0   1
1   38232   2   30  0   1

It doesn't make any sense to me, I manually checked the first variants in the vcf file I get:

13504 present in 1 individual out of 17  
19776 present in 1 individual out of 17
19978 present in 1 individual out of 17
21580 present in 3 individual out of 17
22158 present in 3 individual out of 17

[mks002]

You can try with the varscan, for the readcount. Please follow the link here

/tool/Varscan/VarScan.v2.2.11.jar readcounts <mpileup> --min-coverage 20 --min-base-qual 30 --output-file <output file name>

[WouterDeCoster]

OP is looking at variant frequencies in a vcf, are you sure your question about getting read counts is a relevant answer?

[mks002]

The whole idea is to check for the variants at a particular locus. When getting the read counts for the position, what can be done is you can map the read counts with VCF file and check the exact reads supporting your variant calls.

[Stane]

I am not familiar with varScan but I have only access to the variant vcf files not the mpileup

Answer 1

[Stane]

I kinda figure it out the real freq I was interested in is the the snp population freq and it seems to be N_CHR x right part of FREQ / (2 X polution)