Re: [Vcftools-help] Help Please Counts of individuals

[Laura C. <la...@eb...>]

Hello Kimberly

You should look at the command fill-ac-an

http://vcftools.sourceforge.net/perl_module.html#fill-an-ac

If you subset your vcf file to the individual you are interested in using
vcf-subset then pipe through fill-ac-an it should give you the info you need

try a command like

tabix -h
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr13.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
13:start-end | vcf-subset -c list_samples.txt | fill-ac-an | bgzip -c >
myvariants.vcf.gz

Should leave you with AC (allele count) and AN (Allele number) fields which
match the individuals in the file

thanks

Laura

On 17 April 2015 at 18:47, Kimberly Olney <oln...@ic...> wrote:

> 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
>
>
>
>
>
>
>
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