Re: [Vcftools-help] AC=0

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

Hi Joanna,

These are slightly funny cases, as the alternate allele isn't defined for 3
of the sites. Try using --min-alleles 2 to get rid of those.

Best,

Adam


On Mon, May 26, 2014 at 8:10 AM, Joanna Kelley <joa...@gm...>wrote:

> Hi all,
>
> I have a vcf with non-variable positions, a small example is below. I'd
> like to filter out the non-variable sites. I've tried both the --mac 1 and
> the --non-ref-ac 1 flags, but neither removes those sites. Any advice on
> how to remove the non-variable sites?
>
> Thanks,
> Joanna
>
> #CHROM    POS    ID      REF    ALT    QUAL    FILTER    INFO    FORMAT
> Victoria    9732    ....
> chr1    958777    chr1_958777    C    .    .    .    AC=0;AN=24      GT
> 0/0    0/0    0/0
> chr1    958778    chr1_958778    T    .    .    .    AC=0;AN=24      GT
> 0/0    0/0    0/0
> chr1    958779    chr1_958779    T    .    .    .    AC=0;AN=24      GT
> 0/0    0/0    0/0
> chr1    958780    chr1_958780    A    G    .    .    AC=2;AN=24      GT
> 0/0    0/0    1/1
>
>
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-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
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