Nikos Tsardakas RenhuldtI have #genomic variants called using #FreeBayes. I want to identify sex-linked regions of the genome. As a complement to visualization I’m considering doing some type of #statistical analysis, in part driven by wanting to learn more #stats. I’m less interested in allele differences (GWAS) and more in #heterozygosity, coverage depth, etc. Are there standard models to identify region differences? Could a #MixedModel be used for this?
Bertrand ServinWe have been looking for a simple and fast way of #genotyping a #bam file at known sites that we get from a reference #vcf.
We ended up using #freebayes with -@ -l --report-monomorphic options.
BUT I was quite surprised by the lack of information and clear documentation for performing this seemingly trivial task without going through the whole SNP calling stuff (we don't want to do it).
Did we miss something ? Is there a standard, well documented method out there ?