[Vcftools-help] Help Please Counts of individuals

[Kimberly O. <oln...@ic...>]

Hello, 

I am a little confused on how to get some information that I would like o have. 
What I would like to know is how many individuals have Allele 1(Ref)  vs. Allele 2 (Alt) and if at all possible which individuals. 
so Something like this:

Allele1    Allele2   Count1   Count2   MAF
A		T             90           9          If possible I would like to know how many out of my 99 individuals have the minor allele 2/99? 

I have 99 CEU individuals from the 1000geneome project and am looking at chromosome 13

what I have done so far is gotten allele frequency using and frequency count:

 out.frq
CHROM	POS	N_ALLELES	N_CHR	{ALLELE:FREQ}
13	19020047	2	198	A:1	T:0
13	19020074	2	198	C:1	A:0
13	19020078	2	198	C:1	T:0
13	19020095	2	198	C:0.964646	T:0.0353535
13	19020116	2	198	C:0.994949	T:0.00505051
13	19020125	2	198	C:1	A:0
13	19020165	2	198	T:1	A:0

and 
out.frq.count
CHROM	POS	N_ALLELES	N_CHR	{ALLELE:COUNT}
13	19020047	2	198	A:198	T:0
13	19020074	2	198	C:198	A:0
13	19020078	2	198	C:198	T:0
13	19020095	2	198	C:191	T:7   
13	19020116	2	198	C:197	T:1

Is it possible to get the name/number of that individuals that have allele2? and the count of how many individuals have C vs T? 

Thank you, 
Kimberly