Hi,
I want to genotype known CNVs (from 1000G Phase3, GoNL, etc.) in our samples using GenomeStrip without performing any discovery step at first.
1) Do I have to run only the SVPreprocess steps followed by the SVGenotyper step ? Does the CNVDiscovery and/or LCNVDiscovery pipelines produce metadata that can be useful for the duplications and CNV genotyping or does the SVPreprocess produce all needed metadata ?
2) As far as I understand, imprecise variants are genotyped using the SVTYPE info. The documentation explains SVTYPE=DEL and SVTYPE=CNV. But how does the software consider SVTYPE=DUP ? SVTYPE=INS ? SVTYPE=DEL_ALU and so on which are present in 1000G Phase3 vcf file ? Does SVGenotyper consider all SVTYPE except DEL as CNV so that it will try to genotype different copy number alleles ? If true, does that mean that a SVTYPE=DUP can be genotyped as a deletion for example if GenomeStrip finds it's not a pure duplication (so that we can't force the SVTYPE) ?
Best,