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GenomeSTRiP CNV filtering
I am a little unclear on what the default filtering that was used during the default CNV pipeline.
This is what the CNV vcf file header had:
##FILTER=<ID=ALIGNLENGTH,Description="GSELENGTH < 200">
##FILTER=<ID=CALLRATE,Description="GSCALLRATE == NA || GSCALLRATE < 0.9">
##FILTER=<ID=CLUSTERSEP,Description="GSCLUSTERSEP == NA || GSCLUSTERSEP < 5.0">
##FILTER=<ID=DENSITY,Description="(1.0 * GSELENGTH / GCLENGTH) < 0.5">
##FILTER=<ID=DUPLICATE,Description="GSDUPLICATESCORE != NA && GSDUPLICATEOVERLAP >= 0.5 && GSDUPLICATESCORE >= 0.0">
##FILTER=<ID=GTDEPTH,Description="GSM1 == NA || GSM1 <= 0.5 || GSM1 >= 2.0">
##FILTER=<ID=INBREEDINGCOEFF,Description="GLINBREEDINGCOEFF != NA && GLINBREEDINGCOEFF < -0.15">
##FILTER=<ID=LENGTH,Description="GSCNCATEGORY == NA || (GSCNCATEGORY == DEL || GSCNCATEGORY == MIXED) && GCLENGTH < 1000 || GSC & GCLENGTH < 2000">
All the vcf records had GLINBREEDINGCOEFF=NA, so was the Inbreeding Coefficient actually calculated and used?
Also what is the best approach to add add or modify a filter? Can a new CNV filter be added to the pipeline easily or is it best to filter on the stage12 results.