archaic-introgression

You can detect Neanderthal DNA segments in modern human genomes by running the archaic introgression skill with modern and archaic VCF files. It identifies shared segments using IBDmix, Sprime, or hmmix to map archaic ancestry.

To identify Denisovan ancestry using VCF files, run the archaic introgression skill by passing your modern and archaic VCF files as arguments. It applies IBDmix, Sprime, or hmmix methods to find introgressed segments.

Yes, you need bcftools along with numpy, ibdmix, sprime, and hmmix installed in your environment to analyze archaic introgression. These external dependencies are required to process the VCF files and run the detection methods.

IBDmix and hmmix are both supported methods for finding archaic introgression segments, utilizing different statistical approaches to detect shared ancestry. The skill allows you to utilize any of these methods for comprehensive genomics analysis.

Yes, this archaic introgression detection is designed for genomics research focusing on Neanderthal and Denisovan ancestry across modern human genomes. It processes standard VCF file inputs to identify introgressed segments for disease susceptibility studies.

Your archaic introgression analysis requires both modern and archaic VCF files because the detection algorithms compare modern human genomes against archaic hominin references to identify shared segments. Both inputs are necessary command line arguments.