Uncollapsed gene families

[nicola-palmieri]

Uncollapsed gene families

[gtonkinhill]

Hi Nicola,

This is likely to be mainly due to the diversity and mobility of the gene.

If you have diverse versions of a gene occurring in different regions of the genome it can be very challenging (and sometimes not desirable) to cluster them together. In my experience, annotations of gene families like this one are often inconsistent so I would also expect instance of annotations of different tra* genes to be clustered together in some situations.

By design, Panaroo is cautious about clustering diverse copies of a gene that occur in different locations as these can often have different functions or phenotypes. I would recommend performing two separate GWAS analyses. One using the gene clusters from Panaroo, which will also encode information about location and diversity and one using unitigs as described in pyseer