RTG vcfeval Runs The following report outlines multiple trials attempted to run RTG Tool’s vcfeval using a subset universe, a subset of variants extracted from a Complete Genomics (baseline set) and Manta (call set) VCF files based on NA12878. The Complete Genomics VCF file was generated using proprietary tools from Complete Genomics on a 200x sample (downloaded from CG website), while Manta’s (Illumina SV caller) output VCF was generated using Platinum Genomes 50x; 300 insert size PE data. The subset universe refers to VCF filtered by SVtype, chromosomes, size and highquality variants. The following criteria were used to generate these VCFs, Complete Genomics SV Types: DEL, INS, INV Chromosomes: 1-22 Sizes: 6 ≤ x Filter Flags: PASS, PRECISE, Breakpoint evidence > 10 reads Manta SV Types: DEL, INS, INV Chromosomes: 1-22 Sizes: 6 ≤ x Filter Flags: PASS, PRECISE, QUAL ≥ 30 TRIAL RUNS Notes: 1 The following SDF FILE was used a. 1000g_v37_phase2.sdf from RTG website 2 All “bgzip” and “tabix” indexes necessary to run vcfeval were create were generated with RTG tools a. BGZIP: rtg bgzip b. TBX: rtg index –f vcf 3 Sorting was done through vcf-sort from VCFtools For the following examples just show example command lines used to run the program and the datasets used on each run.

RUN # 1: This run was done between the baseline and call subsets mentioned at the beginning of the document Status=ERROR rtg vcfeval –b CG_subset_universe.vcf.gz \ –c manta_subset_universe.vcf.gz \ -o test \ -t 1000g_v37_phase2.sdf \ -T 1 -b (baseline) Complete Genomics Truth subset universe calls (CG_subset_universe.vcf.gz) -c (calls) Manta Test subset universe calls (manta_subset_universe.vcf.gz) -t (reference) Reference SDF format file from RTG website (1000g_v37_phase2.sdf)

RUN # 2: Afterward, I aimed to check which was the source of the problem and ran the same subset as baseline and call set to see if vcfeval would work Status=SUCCESS rtg vcfeval –b manta_subset_universe.vcf.gz \ –c manta_subset_universe.vcf.gz \ -o manta_vs_manta \ -t 1000g_v37_phase2.sdf \ -T 1

RUN # 3: The Error appeared to be caused by the CG baseline VCF, and after extensive manual curation I still couldn’t determine the exact source of the error. Status=FAIL rtg vcfeval –b CG_subset_universe.vcf.gz \ –c CG_subset_universe.vcf.gz \ -o cg_vs_cg \ -t 1000g_v37_phase2.sdf \ -T 1