Separation and phasing of sex chromosome

[wjhlang]

Hi,

Thank you so much for developing this wonderful tool! I've had success phasing my assembly on autosomes, but I’m encountering an issue with the sex chromosomes: for a male sample, nearly every region covered by a contig on chromosomes X and Y is assigned to both Hap1 and Hap2, as shown below:

I expected to see chromosome X in one haplotype and chromosome Y in the other, i.e. chromosome X only on Hap1 and chromosome Y only on Hap2. Do you have any insights into what might be causing this and how I can resolve it?

Thank you again!
Jason

[mikolmogorov]

Hi Jason,

Sorry for my late response! That's a current limitation unfortunately, hapdup tries to duplicate all chromosomes and does not specifically handle sex chromosomes. I hope to fix this in the future, but for now probably the easiest workaround is to keep just throw away everything in haplotype 2 that aligns to sex chromosomes (if it's a male sample).

[wjhlang]

Hi Mikhail,

Thanks for letting me know! I will use the workaround for now.

Best,
Jason

[WeichenZhou]

Hi @mikolmogorov

Thank you so much for making this tool. As I am following this issue, I am just curious should the sex chromosome be considered as negative control? Would you maybe provide some insights on what introduced this bug? Thank you so much for your time!!

Best,
Arthur

[mikolmogorov]

Hi Arthur - the main reason is that hapdup currently does not have prior knowledge if there is 1 or 2 copies of chrX, and doesn't know which contigs correspond to chrX in general. It aims to phase all input contigs.

[WeichenZhou]

Hi Mikhail,

Thanks for the reply. Now I get what you mean and see the logic of how hapdup works. Thank you so much for your tool! Hopefully, it can be patched.

Best,
Arthur