I read this sentence in one article: "After excluding samples that failed to reach 95% call rate for all assays". What does "call rate" mean? And Why do the author only include samples with a SNP genotype call rate of ≥95%? Thank you.
'Call rate' is the proportion or percentage of samples in which a confident genotype call could be made. 95% is a typical value.
In the other samples in which a call could not be made, the probes may have failed, resulting in no binding to the template DNA. It is also possible that the DNA was lesser quality in these samples, or non-existent, for whatever reason(s).
Why 95%? - it's an arbitrary cut-off. It means that the maximum missingness that we want to tolerate for any SNP is 5%.
Kevin
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version 2.3.6
Hi, It is a standard GWAS practice to exclude samples/individuals that have missing genotype data across more than a pre‐defined percentage of the typed SNPs (95% in this case). You might find these papers interesting
A guide to genome‐wide association analysis and post‐analytic interrogation
A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis
Quality Control Procedures for Genome Wide Association Studies
Genome-Wide Association Studies