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SNV concordance between tumor-organoid pairs was determined from the overlap of variant calls and variant allelic fractions. For each SNV called in the tumor or organoid, we ran Samtools Pileup (with minimum base quality and minimum mapping quality of 10) at this position for both samples to compute the variant allele fractions. If read evidence for the SNV was present in both samples (and therefore VAF>0), the SNV was considered concordant. To add confidence to this analysis, we only included SNVs that were called by 2 or more variant callers in at least one of the samples.
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