How to set-founders

[dwill023]

Hi, I would like to know how I can specify the Ped-sim founder id for the --set_founders option.

I have simulated a pedigree and I have individuals within the pedigree I would like to specify a founder for. Below is a table of some of the individuals in the pedigree and the numbers of the kinship degree.

I'm interested in specifying individual F1_g4-b1-i1 as a founder as it has many relationships at different degrees. Is this possible or am I using --set_founders wrongly?

[williamslab]

The --set_founders option is used in combination with an input VCF file. It allows you to specify which individuals in the input VCF Ped-sim should assign to each of the founders.

[dwill023]

OK I think I figured it out when I run with the flag --founder_ids that shows which samples were randomly assigned to a founder.
Can you state in the readme, if I'm not wrong, the simulation starts with two founders in generation 1 and when we want to specify the --set-founders the ped-sim id is an individual with an s[#]. I know this may be implied in the section Sample ids for simulated individuals but just having it restated under the Assigning VCF ids to specific founders: --set_founders section really helps.

[williamslab]

I can add that, but the individuals you'd be assigning are i1 and s[#], not only the s[#]. Just wanting to make sure we're on the same page before I make the change.