Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Using GenomeStrip to genotype known vcf
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) ?