how to filter a multi-VCF for sex-specific genotypes?
Found a great tool with SnpSift!

From the examples: I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference:

cat variants.vcf | java -jar SnpSift.jar filter "isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )" &gt; filtered.vcf