incorrect expected relatedness for consanguineous family

brentp / peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

MIT License

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incorrect expected relatedness for consanguineous family #56

Open ekarlins opened 5 years ago

ekarlins commented 5 years ago

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 commented 5 years ago

can you share the ped file?

ekarlins commented 5 years ago

@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 commented 5 years ago

bpederse@gmail.com . thank you.

ekarlins commented 5 years ago

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

Thanks! Eric

holtgrewe commented 5 years ago

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 commented 5 years ago

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.