Re: [Vcftools-help] No output to vcftools --keep-filtered

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

Hello Michael,

You have not told vcftools to do anything beyond read the file in. If you
would like vcftools to generate a vcf file containing just the filtered SNP,
you need the --recode command as well.

Hope that helps,

Adam

On 15 December 2010 18:16, Michael Jones <mdj...@gm...> wrote:

> I run the following command with the following output, however, there
> is no out file and my input file is not modified. Any Ideas where the
> output went?
>
> jonesmic@illumina1:humanize $ ~/sequence-tools/VCF/cpp/vcftools
> --keep-filtered NoRefSeq --vcf ./snps.mcl.short.test.vcf --out shug
>
> VCFtools - v0.1.3.1
> (C) Adam Auton 2009
>
> Parameters as interpreted:
>        --vcf ./snps.mcl.short.test.vcf
>        --out shug
>        --keep-filtered NoRefSeq
>
> Scanning ./snps.mcl.short.test.vcf ...
> Warning: Commas in FORMAT description.
> Warning: Commas in FORMAT description.
> Warning: Commas in INFO description.
> Warning: Commas in INFO description.
> Warning: Commas in INFO description.
> Warning: Commas in INFO description.
> Warning: Commas in INFO description.
> Currently scanning CHROM: chrM
>        Keeping 177 entries (out of 177 read)
> Done
> Filtering sites by FILTER Status.
> Kept 4 out of 4 Individuals
> Kept 1 out of 177 Sites
> Run Time = 0.00 seconds
>
>
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