 To identify the number of heterozygous variants in my .vcf file, I used the following linux command in vcftools:

     $ vcftools --vcf SRR1611183.gatk.vcf --het

And returned the following:

    INDV	O(HOM)	E(HOM)	N_SITES	F
    NA12878	0	0.0	1101	0.00000

This is the same as the **'het_RA_count' => 1101** found in the `vcf-stats` feature; however, `vcf-stats` also lists **'het_AA_count' => 2**, which is not included in the `--het` command.  If I'm seeking the total number of heterozygous variants should I just total them up (to 1103)?  Perhaps het_AA is not truly heterozygous?

I'm open to a bcftools solution if its more straightforward.


You can try my 'independent' script and see what it returns: https://www.biostars.org/p/291147/#291167

That just counts the occurences of `0/1` `1/0` `0|1` and `1|0` per line. The total heterozyguos calls in the file will be the total of the final output column.

Another, more complex version of this is here: https://www.biostars.org/p/298361/#298464

Note that you should indeed be using BCFtools and not VCFtools. I believe that this advisory is even given by the VCFtools author (Adam).

Kevin
