Haplotype input naming and using primary assembly as reference

[hrluo93]

Hi,

Thank you for developing this great tool.

I would like to ask for clarification about how haplotype inputs are handled in Minigraph-Cactus.

My understanding is that if haplotypes are named as SAMPLE.1 and SAMPLE.2, Minigraph-Cactus will recognize them as two haplotypes from the same diploid sample, rather than as two independent samples. Is this correct?

I also have another question about the reference. If I use the primary assembly of one individual as the reference, can the two phased haplotypes from that same individual still be added as separate inputs when constructing the graph? Or would that be considered redundant / duplicated representation of the same sample?

Like this:
ref-sample.P ref.T2T.primary.fa ← Primary chromosome-level near T2T as reference and ref-sample.P will not be present in VCF
ref-sample.1 ref.hap1.fa ← Reference sample hap1 contigs
ref-sample.2 ref.hap2.fa ← Reference sample hap2 contigs
indv2.1 indv2.hap1.fa ←indv2 hap1 contigs
indv2.2 indv2.hap2.fa ←indv2 hap2 contigs
...

Or should I do:
ref-sample.1 ref.hap1.fa ← Reference sample hap1 as reference, re-scaffold to chromosome-level near T2T
ref-sample.2 ref.hap2.fa ← Reference sample hap2 contigs ? But will this present only one hap in VCF?
indv2.1 indv2.hap1.fa ←indv2 hap1 contigs
indv2.2 indv2.hap2.fa ←indv2 hap2 contigs
...

Best Wishes!
Haoran

[glennhickey]

Hi, this is a good, and frequent question. The haplotype numbers impact the vcf creation and not much else. I personally lean toward the second option:

ref-sample_1 (reference)
ref-sample.2

Your vcf will have fields like .|1 .|0 etc for ref-sample. But there is nothing preventing you from doing

ref-sample_1 (reference)
ref-sample.1 
ref-sample.2

Your ref-sample variants will be 0|1 0|0 now instead of .|1 .|0 in the VCF and you will have a redundant path in your graph.

[hrluo93]

Hi, this is a good, and frequent question. The haplotype numbers impact the vcf creation and not much else. I personally lean toward the second option:

ref-sample_1 (reference)
ref-sample.2

Your vcf will have fields like .|1 .|0 etc for ref-sample. But there is nothing preventing you from doing

ref-sample_1 (reference)
ref-sample.1 
ref-sample.2

Your ref-sample variants will be 0|1 0|0 now instead of .|1 .|0 in the VCF and you will have a redundant path in your graph.

Thanks for your reply. This is very helpful. Minigraph-Cactus is a great tool, and really appreciate your clarification.

Best!