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Table 2 Call concordance with the 1000 Genomes Project (homozygous common allele)

From: Comparison of genotype clustering tools with rare variants

Tool

NA12763 _R

NA12763 _R1

NA12763 _R2

 

Rate

Number

Rate

Number

Rate

Number

GenCall (original)

0.999478

114,975

0.999461

115,008

0.999486

114,876

GenCall (optimized)

0.999393

115,288

0.999384

115,288

0.999393

115,279

GenoSNP (original)

0.999630

97,236

0.998973

78,868

0.925482

74,210

GenoSNP (optimized)

0.999190

114,814

0.999138

114,910

0.999207

114,687

optiCall

0.998990

114,815

0.998972

114,805

0.999006

114,701

zCall

0.999281

115,438

0.999281

115,437

0.999290

115,438

  1. Call concordance and number of compared markers for the three control replicates when compared to the 1000 Genomes Project. For each dataset (i.e. tool), only genotypes called as homozygous of the common allele (according to the allele frequency computed using the corresponding dataset) were kept for analysis. The following six tools were compared: GenCall (original and optimized cluster files), GenoSNP (original and optimized), optiCall (without excluding markers failing Hardy-Weinberg) and zCall.