Dear Bioconductor team, I am contacting you because for my PhD project we have done whole genome sequencing with 30x coverage of 50 patients. We got the fastq files from the sequencing facility and now I am working on the annotation and analysis of this data set.

We used ANNOVAR and the hg38 gnomAD databases for the data annotation. I looked all over your website and also the FAQ section but I could not find any information about whether or not the SeqSQC package is compatible with/can handle hg38, could you please let me know where to find this?

I would truly appreciate your guidance regarding this matter.

Thank you in advance for your time and support, Itzel

I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on the genome build?