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Table 2 Number of biallelic SNPs discovered on chromosome 1 with low sequencing coverage with different GATK HaplotypeCaller pruning options, the percentage of variants not validated with high sequencing coverage, and genotype and allele concordances with the SNP genotyping array

From: Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

  minPruning = 2 (default) minPruning = 1
Number of variants 1,333,943 1,877,644
Not validated at high coverage 3.1% 24.1%
Best-guess genotype concordance 62.1% 76.5%
Allele concordance 77.6% 87.5%