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Table 1 Switch error rates in phasing the HapMap2 samples with SHAPEIT on the original 2.6 million SNPs and on a reduced panel of around 55,000 SNPs

From: Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium

HapMap2 panel

Switch error rates

 

Original density

Reduced density

JPT + CHB

1.5%

12.5%

CEU

1.0%

9.6%

YRI

5.1%

10.2%