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Particular attention should be paid to complex variants as there is typically variability in the manner in which they are documented. For example, we detected 32 loci that had distinct alternative alleles between various cell lines. When pooled into Sample A, these will appear as multi-allelic variants. For simplicity for analytical performance calculations and given the small magnitude of these variants, they were removed from our official positive variant list. However, we are quite confident in our assessment that these 32 loci are multi-allelic in Sample A and those 32 loci (64 variants) are provided in Additional file 1: Table S11. In addition to multi-allelic variants, we have also documented certain SNVs/indels in phase with other SNVs/indels which could be properly termed MNVs. Our list of positives includes over 200 dinucleotide and some trinucleotide positions that can more properly be termed as MNVs as well as other potential MNVs.

When evaluating the performance of cancer panels, it is important that proper guidelines and tools be used relative to the known content of complex reference samples [99]. We recommend using tools such as RTG vcfeval when reviewing panel results with Sample A positives to resolve the ambiguities with multiple representation of variants so that false positive and false negatives are best characterized.

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