Re: [Vcftools-help] (no subject)

[Adam A. <ada...@gm...>]

The chromosome in your vcf file is called "chr1", not "1". You therefore
need to use --chr chr1 in your command.

On Mon, Apr 20, 2015 at 2:30 PM, Younes Miar <mi...@ua...> wrote:

> Hello everyone,
>
> I am using this command to extract SNPs in chromosome 1 only
>
> vcftools --vcf geno_final2.vcf --chr 1 --out subset
>
> Here is the log file:
>
> VCFtools - v0.1.12b
> (C) Adam Auton and Anthony Marcketta 2009
>
> Parameters as interpreted:
>         --vcf geno_final2.vcf
>         --chr 1
>         --out subset
>
> Second Header entry should be POS:
> Third Header entry should be ID: POS
> Fourth Header entry should be REF: ID
> Fifth Header entry should be ALT: REF
> Sixth Header entry should be QUAL: ALT
> Seventh Header entry should be FILTER: QUAL
> Eighth Header entry should be INFO: FILTER
> Ninth Header entry should be FORMAT: INFO
> After filtering, kept 9689 out of 9689 Individuals
> After filtering, kept 0 out of a possible 19 Sites
> No data left for analysis!
> Run Time = 0.00 seconds
>
>
> The geno_final file is like this:
>
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HO840M3001697380
> HO840M300169749
> chr1 100021883 BTA-45212-no-rs C T 999 . . GT 1/1 1/0
>
> I have 6 SNPs in CHR 1, however VCFTOOLS gives me no sites.
>
> I would be highly appreciated if you could help me on this please?
>
> Best Regards,
> Younes
>
>
>
>
>
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-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
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