Admixtools Utilizing AI for WGS30x FASTQ-Plink conversion & AADR Merge for Downstream Analysis in Admixtools2

[Jovialis]

I'm going to have to learn how to do this all over again when the Reich Lab updates the AADR dataset.

Next time around I'll take better notes. The first time around was a lot of trial and error, as well as uncertaintly.

Next time around, I will at least have the confidence of knowing it is indeed achievable, since I did it before.

 

[Jovialis]

^^Ultimately, the goal of this thread was not only to document the process, but to also serve as a guide. While I was successful in facilitating the conversion, I failed at documenting the process so it could be replicated easily. The main reason for this was the uncertainty led me down some rabbit holes. Nevertheless, I will make sure accomplish the full-scope of this thread, and create a guide.

 

[Maroc25678]

For the guy who said to just use the combined kit file from wgs extract it doesn’t work, reason being it’s a weird file with a whole load of duplicates and even after you remove the duplicates it has strange file sizes not allowing you to flip the snps when merging it with the dataset.

 

[Jovialis]

I successfully replicated the process with high coverage and complete integrity of the AADR intact:

Thread 'Modern FASTQ to Eigenstrat Format with AADR Merge'

Apr 1, 2025

This bioinformatics pipeline processes raw genomic data from paired-end FASTQ files to generate merged genotype data compatible with the AADR (Allen Ancient DNA Resource) dataset, enabling population genetics analysis. It begins by setting up a working environment and installing essential tools like samtools, bwa, fastp, Picard, pileupCaller, and EIGENSOFT. The pipeline then downloads and prepares the GRCh37 reference genome (with decoy sequences), adjusts its FASTA headers, and indexes it for alignment. Paired-end FASTQ files are trimmed and filtered using fastp, aligned to the reference...

• Jovialis

•