[Vcftools-help] AC=0

[Joanna K. <joa...@gm...>]

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