how to allele-specific methylation calling?

[sahuno]

Hi,
may i inquire how to do allele specific/happlotype resolved methylation calling and analysis? a look in the literature requires phasing tools like whatsapp etc...
i already did base calling 5mc_5hmC dorado then methylation calling with modkit.

thanks in advance
-S

[ArtRand]

Hello @sahuno,

In order to perform haplotype-specific methylation analysis, you'll need to use a phasing tool like whatshap first. The output of this tool should be "haplotagged" reads where each phased read has a HP tag usually HP:1 and HP:2 indicating the two haplotypes. Then you can use modkit pileup --partition-tag HP and you'll get a pileup for HP:1 and HP:2 separately. Then you can use the differential methylation command to sites that are different (i.e. haplotype specific).

[sahuno]

thanks!