SeqSQC can be used for sample QC of Whole Genome Sequencing Data

Question

[ttom]

I am using the R librabry SeqSQC from Bioconductor to do sample QC of around 50 Whole Genome Sequencing samples.

The vignette says Through incorporation a benchmark data assembled from the 1000 Genomes Project, it can accommodate NGS study of small sample size and low number of variants.

https://www.bioconductor.org/packages/devel/bioc/vignettes/SeqSQC/inst/doc/vignette.html

I could generate plots for MissingRate, SexCheck, Inbreeding, IBD, PCA, . Not sure if WGS samples with high coverage are giving the right results.