SVFiltering¶
- GenomeSTRIP Tutorial July 2013
http://software.broadinstitute.org/software/genomestrip/sites/default/files/materials/GATKWorkshop_GenomeSTRiP_tutorial_July2013.pdf - An integrated map of structural variation in 2,504 human genomes: Suplemmentary materials
http://www.nature.com/nature/journal/v526/n7571/extref/nature15394-s1.pdf - Whole-genome sequence variation, population structure and demographic history of the Dutch population (GoNL project) : Suplemmentary materials
http://www.nature.com/ng/journal/v46/n8/extref/ng.3021-S1.pdf - see also for genomestrip
https://sourceforge.net/p/svtoolkit/mailman/message/28046131/
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 :