...
Now find which GT are hom in both of the second two (parents) but het in the first (child):
Code Block join NA12892.raw.vcf.simple.hom NA12891.raw.vcf.simple.hom > both.hom join both.hom NA12878.raw.vcf.simple.het | wc -l
Virmid - an advanced auto-screener
GATK also has a host of VCF related screeners/joiners/overlapers etc.