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Table 1 Call concordance with the 1000 Genomes Project (all calls)

From: Comparison of genotype clustering tools with rare variants

Tool

NA12763 _R

NA12763 _R1

NA12763 _R2

 

Rate

Number

Rate

Number

Rate

Number

GenCall (original)

0.998591

127,062

0.998623

127,093

0.998425

126,980

GenCall (optimized)

0.998963

127,323

0.998963

127,323

0.998979

127,312

GenoSNP (original)

0.966771

113,365

0.907042

97,345

0.762193

93,555

GenoSNP (optimized)

0.996161

126,848

0.996446

126,893

0.995795

126,748

optiCall

0.995421

127,334

0.995413

127,323

0.994995

127,277

zCall

0.998785

127,545

0.998793

127,544

0.998785

127,545

  1. Call concordance and number of compared markers for the three control replicates when compared to the 1000 Genomes Project. 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.