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As described in the main text, NIST has, through their Genome-in-a-bottle (GIAB) program, made available at ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ variants and high-confidence genomic calling regions for (at the time) five distinct persons. High confidence for GIAB samples was achieved by several methods, of which the initial primary results were from determining consensus among distinct library preps (including 10X Chromium preps), sequencing, (e.g., sequencing platforms typically involved Illumina, Ion Torrent, and SOLID), and variant calling methods. The genome HG001 (aka NA12878), had additional data from more sequencing platforms and additional review to identify extended regions from the initial consensus for what was viewed as “high-confidence” calls for that genome. Due to this special case of additional data and review of the high-confidence regions, the SEQC2 consortium instead examined the high-confidence regions for HG002, HG003, HG004, and HG005 (all v3.3.2) and their overlap for hg19 and hg38, respectively. The overlap in high-confidence regions between any pair of this set was greater than 95% while the overlap in high confidence of any member of the set with HG001 was usually less than 91% of HG001 due to its much larger size and that HG001 includes chrX while the others did not. The final region selected as the high-confidence region for this study for the individual cell lines and their mixture was the intersection of the high-confidence regions of HG002-HG005. Although we performed parallel discovery and validation for hg19 and hg38, the positives are primarily determined using the high-confidence region of hg19 as hg38 is noticeably smaller in size.

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