Phasing human samples with Shapeit4

Question

[Private]

I'm currently working with a set of files of human samples that I've converted from PLINK format to VCF. My objective is to phase them using Shapeit4, specifically without the --map flag, aiming for a phasing density of 1cM/mb.

I've automated the phasing for each chromosome and subsequently concatenated these segments into a single VCF file, which I then attempt to recode back to PLINK format. Unfortunately, I'm encountering issues with the coverage post-phasing—it appears to be compromised.

Could anyone advise on potential mistakes I might be making or suggest any additional steps I should consider? Any insights or advice would be greatly appreciated. Thank you!

[bk11]

Could you please tell us what is your plan post phasing your data?

[Private]

I'd like to run it on GERMLINE IBD and other programmes that required phased input files. It's just the phasing with Shapeit4 isn't outputting a properly phased singular file of course, It goes by each chromosome, so my hunch is perhaps the concatenation is going wrong here?