Reference TR-CNV variants for TR-CNV evaluation

The files, sim_TR_DEL.chr1.vcf.gz, sim_TR_INS.chr1.vcf.gz, and sim_non-TR-INS.chr1.vcf.gz contain ~1,000 simulated TR-DEL, TR-INS, and non-TR-INS variants used to evaluate TR-CNV detection tools in our paper, respectively. The variants for each TR-CNV type were introduced into existing TR sites on diploid chromosome 1 of the human GRCh38 reference genome, artificial 20x PacBio HiFi long reads were created. The half (~500) of non-TR-INSs were mobile elements (i.e., ALU, L1, and SVA) and the other half were tandem repeats with repeat units unrelated to those of the introduced TR sites. These vcf files were used as the reference variant data for the evaluation using simulated data.

HG002_GRCh38_TandemRepeats_v1.0.1.matched.ml50.filt.vcf.gz and HG002_GRCh38_TandemRepeats_v1.0.1.non-TR-INS.ml50.vcf.gz were used as the reference of real data for the evaluation of TR-CNV detection tools. These variants are curated TR-CNVs and non-TR-INSs selected from the GIAB HG002 GRCH38-based TR-CNV catalog.