incorrect expected relatedness for consanguineous family

[ekarlins]

I have a family where the parents are first cousins. I gave Peddy an extended pedigree and it was able to distinguish the parents as cousins, which matches the calculated coefficient of relatedness (the parents are the green dot on the plot below). However, the children were all given an expected relatedness of 0.031, though the pedigree clearly lists both parents for each child. They are the orange dots on the plot below. I'm using Peddy v0.3.1.

Thanks! Eric

[brentp]

can you share the ped file?

[ekarlins]

@brentp Thanks for your reply! I think I can share the ped file, but need to check with some others in my group to make sure that's ok. Is there an email address that I can send it to?

Thanks, Eric

[brentp]

[email protected] . thank you.

[ekarlins]

I emailed you the ped file. Let me know if you didn't get it.

Thanks! Eric

[holtgrewe]

Hi, I'm also having this issue. Is there any news? Peddy is such a useful tool and I would really appreciate a bugfix. Thank you.

[brentp]

hi, I'll try to get around to fixing this. Meanwhile, you can use somalier where I have resolved this problem. It has similar output to peddy and can be use directly on VCF or on the bams.