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

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

Hello, 

Thank you for getting back to me. I was able to subset which individuals I wanted but the -fill-ac-an didn’t work 

$ tabix -h /Users/olneykimberly/Desktop/13/ALL.chr13.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz 13:start-end | vcf-subset -c /Users/olneykimberly/Desktop/13/integrated_call_samples_v3.20130502.ALL.panel | fill-ac-an | bgzip -c > myvariants.vcf.gz
-bash: fill-ac-an: command not found

I tried this on my already subset vcf file, on the original command listed below with my list_samples.txt, and one a already downloaded chr13.vcf file and I get the same error everytime. -bash: fill-ac-an: command not found

Thank you for your help!

Best, 
Kimberly 


> On Apr 17, 2015, at 12:00 PM, Laura Clarke <la...@eb...> wrote:
> 
> Hello Kimberly
> 
> You should look at the command fill-ac-an
> 
> http://vcftools.sourceforge.net/perl_module.html#fill-an-ac <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 <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... <mailto: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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