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ambiguous explanation of -invMv for SelectVariants

timflutretimflutre Montpellier, FranceMember

Hello,
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:

  • -mv means "Output mendelian violation sites only";
  • -invMv means "Output non-mendelian violation sites only";
  • -mvq means "Minimum GQ score for each trio member to accept a site as a violation".

I hence conclude the following:

  • -mv alone means "generate a VCF of only the variants that are mendelian violations";
  • -invMv means "generate a VCF of only the variants that are not mendelian violations";
  • -mv -invMv is not unambiguously defined, does -invMv take precedence over -mv?;
  • -mv mvq 50 means "generate a VCF of only the variants that have QUAL > 50 and that are mendelian violations";
  • -invMv mvq 50 means "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?

Best,
TF

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