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Table 1 Genotype concordance between WES genotypes and exome array genotypes in 10 samples

From: Effective filtering strategies to improve data quality from population-based whole exome sequencing studies

Filters Number of concordant genotypes Number of discordant genotypes Concordance % of concordant genotypes removed % of discordant genotypes removed
Genotype Variant
None None 73,537 (621,855) 551 (661) 99.26% (99.89%) NA NA
None VQSR 73,069 (608,065) 493 (108) 99.33% (99.98%) 0.64% (2.22%) 10.53% (83.66%)
DP None 72,104 (611,606) 236 (627) 99.67% (99.90%) 1.95% (1.65%) 57.17% (5.14%)
GQ None 72,689 (610,682) 225 (460) 99.69% (99.92%) 1.15% (1.80%) 59.17% (30.41%)
DP & GQ None 71,986 (610,108) 220 (446) 99.70% (99.93%) 2.11% (1.89%) 60.07% (32.53%)
DP & GQ VQSR 71,552 (597,070) 168 (36) 99.77% (99.99%) 2.70% (3.99%) 69.51% (94.55%)
  1. Non-reference genotypes are shown above reference genotypes in brackets.
  2. Non-reference genotypes include genotypes that are heterozygous or homozygous alternate in the exome array. Reference genotypes include genotypes that are homozygous reference in the exome array.
  3. Includes heterozygote to homozygous alternate mismatches.
  4. (See Additional file 1).