Has anyone used the SV caller manta? I have a couple of questions regarding the splitting/spanning reads reported by manta:
1) In the manta output 'diploidSV.vcf', there are PR and SR tags, which mean 'Spanning paired-read support for the ref and alt alleles in the order listed' and 'Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999', respectively. If I want to pull the information for FUSION-SUPPORTING splitting reads, should I use only the SR:ALT or (SR:ALT + SR:REF)? What do the PR:REF and SR:REF reads mean? 2) I was using the default configuration file to run manta, in which, minCandidateSpanningCount = 3 and minEdgeObservations = 3. Why do I still see SVs like below lines kept in the diploidSV.vcf:
as the SR:ALT is 0, and I thought minEdgeObservations = 3 is applied on SR:ALT, or did I understand it wrong?