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Another 4 families were excluded after genotyping because of Mendelian errors.
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As expected, the frequency of Mendelian errors diminishes as a function of increased sequence depth.
Then we examined the relationship between the number of Mendelian errors detected for each SNP and the deviation from HWE.
No samples or SNPs were excluded on the basis of Mendelian errors (overall Mendelian error rate 0%).
Aside from elimination of Mendelian errors, no quality control steps were performed for Affymetrix genotyping data.
PedCheck (O'Connell and Weeks, 1998) was used for detection of Mendelian errors.
The number of mendelian errors ranged from 24 to 132, with an average of 63 errors per pair.
Genotypes of Mendelian error were eventually excluded from the analysis.
Over 1M SNPs were called for all five family members, with low rates of Mendelian error (Table S2 in Supplement 1).
Even though evidence of deletion Mendelian errors are more probable, we would still expect to find non-evidence of deletion Mendelian errors for poorly genotyped SNPs.
For these reasons, we may filter out SNP sites with many non-evidence of deletion Mendelian errors to reduce false-positive rates from systematic errors.
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