QC methods for next generation sequencing samples

Question

[MAPK]

I have been trying to find some papers that discuss quality control on Next generation sequencing samples. I know a lot of paper that discuss about QC on SNPs data, but none on QC of samples. I think P-link is one of the popular tools for this. Can someone please help me find the right papers and available tools used in QC of Samples.

[Devon Ryan]

Do you mean something like FastQC or some other sort of QC?

[MAPK]

No, in terms of IBD and relatedness where we use these QC for correcting confounding biases, but not limited to or exactly of GWaaS studies

[MAPK]

No, in terms of IBD and relatedness where we use these QC for correcting confounding biases, but not limited to or exactly of GWaaS studies

[Devon Ryan]

Ah, you might want to add that to your post and update the title.

Answer 1

[WouterDeCoster]

Relatedness can be studied using either ersa2.0 (http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004144)(rather complicated) or something as simple as PCA.