Open junyanzho opened 4 years ago
I guess your query set has no indels in it, which is why those columns are empty. As for why the INDEL TRUTH.TP is greater than zero even though your query set does not contain indels, see https://cdn.rawgit.com/RealTimeGenomics/rtg-core/master/installer/resources/core/RTGOperationsManual/rtg_command_reference.html#benchmarking-performance-for-snps-versus-indels
Dear developer, I compared trueset file NA12877.vcf.gz( including SNP and IDNEL variants) with query file(only SNP variants). For the INDEL in summary.csv, there are numbers on TRUTH.TP TRUTH.FN columns, while QUERY is zero. summary table as below: