SVFiltering

Selection criteria

  • non duplicate sites (see genomeSTRIP documentation)
  • call rate > 0.8 : proportion of genotyped individuals with GQ> 13 is > 80%
  • at least one variant (homozygous or heterozygote) has a genotype quality > 20
  • the variant is not everywhere heterozygote or homozygote (use NONVARIANTSCORE in both cases)
  • sv with no overlap with CNVR filtered out by genomeSTRIP

The selected variants should be next regenotyped ?

see also (DEPTHRATIO / DEPTHPVALUE)
https://sourceforge.net/p/svtoolkit/mailman/message/28046131/

Visualizing data :

https://github.com/RCollins13/CNView#cnview-summary