[help] Can Bismark handle diploid reference genome please?

[lizhe-gis]

Dear Felix,

Thank you so much for developing this great tool! I rely Bismark heavily for my research :)

Recently we developed a haplotype-resolved diploid human genome, where one copy is paternal and the other copy is maternal. I imagine if I map WGBS data to this reference genome, most reads will have secondary alignment due to the high similarity of pat-/mat-genome. I understand bowtie2 and HISAT2 are both able to randomly assign, but from reading the previous posts and the alignment flags, I understand that currently --ambig_bam will not give any methylation information.

Would it be possible to ask Bismark to randomly assign to one location and include methylation information if the two alignments have exactly the same and highest possible match please?

Thank you very much!

Best Regards, Zhe