vcftools 012 output missing homozygous minor genotype

Question

[boris]

It seems that my .012 file never has any 0 entries (homozygous minor) when run on a sample of over 300 vcf files. I'm looking at common variants. What am I doing wrong?

vcftools --gzvcf combined.vcf.gz --maf 0.05 --max-maf 0.5 --hwe 1e-8 --minQ 40 --012 --max-missing 0.95 --chr chr12 --out combined.chr12.common

VCFtools - v0.1.13
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
        --gzvcf combined.vcf.gz
        --chr chr12
        --maf 0.05
        --max-alleles 2
        --max-maf 0.5
        --hwe 1e-08
        --minQ 40
        --max-missing 0.95
        --012
        --out combined.chr12.common

[Ram]

Is this solved? --max-alleles argument not recognized

[boris]

Nope, although I did figure out that I didn't actually want max-alleles in this particular case. It's still strange that it doesn't seem to work.

[vvividhya93]

Should the vcf files be sorted before running the command given below?

vcftools --gzvcf combined.vcf.gz --maf 0.05 --max-maf 0.5 --hwe 1e-8 --minQ 40 --012 --max-missing 0.95 --chr chr12 --out combined.chr12.common

Because am getting an error like this:

VCFtools - UNKNOWN
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --gzvcf 4fam_vcf_forMDR.tar.gz
    --012

Using zlib version: 1.2.8
After filtering, kept 0 out of 0 Individuals
Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.

[tkloppe]

I encountered the same problem with a gvcf file called with GATK on haploid genome samples.

I only find “-1” for missing data which makes, sense. However, the 1’s represent both alternate allele and reference allele. The “0” for actual reference alleles are missing.

I can provide more info on whatever may help.