Best Practices - ADMIXTOOLS2 Functions: extract_f2/f2_from_precomp, qpWave, qpadm

[Jalisciense]

As usual good job and great answers!

I have some questions, What is maxmiss and how to use it in qpAdm AdmixTools1?

And what about that too?

"F2 Extraction:
extract_f2() creates a precomputed f2 dataset from your raw genotype data, using a lenient setting (maxmiss = 1) to retain as many SNPs as possible. This approach is optimal for aDNA because of its typically high missingness."

 

[Jovialis]

As usual good job and great answers!

I have some questions, What is maxmiss and how to use it in qpAdm AdmixTools1?

And what about that too?

"F2 Extraction:
extract_f2() creates a precomputed f2 dataset from your raw genotype data, using a lenient setting (maxmiss = 1) to retain as many SNPs as possible. This approach is optimal for aDNA because of its typically high missingness."

Frankly, I don't have any experience with Admixtools 1.

But when you set maxmiss to 1 in the pre-computation it basically keeps most of the SNPS, the lower 0.1 it is more restrictive. But with aDNA, it is typically set to 1.