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Gleeson-Lab / wxs_pipeline

Starting with BAMs and FASTQs, follow GATK 4.0 Best Practices up to generating a joint-genotyped VCF
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Implement Confirming Relatedness when a PED file is provided #2

Closed brcopeland closed 3 years ago

brcopeland commented 3 years ago

This should confirm, for child-parent relationships, relatedness in the range of 0.4-0.6. For individuals with the same parents, relatedness should be at least 0.4 (it could theoretically be another sample from the same individual or non-dizygotic twins).

I think it should also flag cryptic relatedness, say greater than second-degree cousins (~0.08 relatedness) in samples from purportedly different families.

brcopeland commented 3 years ago

This is now implemented. I will document in the near future how it works.