ambiguous explanation of -invMv for SelectVariants
on the SelectVariants doc page (here), it is written that the following command:
java -jar GenomeAnalysisTK.jar \ -T SelectVariants \ -R reference.fasta \ -V input.vcf \ -ped family.ped \ -mv -mvq 50 -invMv \ -o violations.vcf
corresponds to: "Generating a VCF of all the variants that are not mendelian violations. The optional argument '-mvq' together with '-invMv' restricts the selection to sites that have a QUAL score of 50 or less".
Moreover, below, the options are described and it is written:
-mvmeans "Output mendelian violation sites only";
-invMvmeans "Output non-mendelian violation sites only";
-mvqmeans "Minimum GQ score for each trio member to accept a site as a violation".
I hence conclude the following:
-mvalone means "generate a VCF of only the variants that are mendelian violations";
-invMvmeans "generate a VCF of only the variants that are not mendelian violations";
-mv -invMvis not unambiguously defined, does
-invMvtake precedence over
-mv mvq 50means "generate a VCF of only the variants that have QUAL > 50 and that are mendelian violations";
-invMv mvq 50means "generate a VCF of only the variants that have QUAL > 50 and that are not mendelian violations";
-mv -mvq 50 -invMv(as in the example above) is ambiguous.
Am I right? If not, can you explain to me the meanings of these various options?