Adding CMT1A-REP region

[alexandra-al1]

Hi,

Thank you for this great tool! I was wondering whether you would consider adding the CMT1A-REP region in the near future. One paralogous copy is located within the COX10 gene and another within FBXW10B in chr17.

Many thanks!

[xiao-chen-xc]

Hi @alexandra-al1

CMT1A-REP copies (roughly chr17:14170712-14194725 and chr17:15567589-15591588, hg38) are 98.2% similar in sequence. HiFi read alignments should be accurate at this sequence similarity. So you can trust the variant calling results of a standard HiFi WGS workflow. There is no need to use Paraphase. If you do find misalignments in this region, it'd be great if you could share an example with me.

Thanks,
Xiao