Running Mixture Deconvolution

Mixture deconvolution utilizes EuroForMix (EFM).

There are several options/settings to run EFM mixture deconvolution:

The type of mixture deconvolution analysis to perform (one or both can be selected at once):
- Unconditioned analysis
- Conditioned analysis

Allele Frequency Data: The user must choose which allele frequency data to use:
- 1000 Genomes Phase 3 data
- gnomAD v4 data
- AFR 1000G data
- AMR 1000G data
- EAS 1000G data
- EUR 1000G data
- SAS 1000G data
The user may also upload a custom file. See Required Files page for more details about the format for uploading a custom AF file.

References to Condition on: IF running a conditioned analysis, once the reference folder has been uploaded, this dropdown menu will auto-populate containing the reference sample IDs. The user must select which references to condition on. As of now, MixDeR can only condition on a single reference sample. However, multiple references can be selected for conditioning; the conditioned analyses will be run separately.

Number of SNP Bins: The number of SNP sets for each sample. The default is 10.

Static Analytical Threshold: The minimum number of reads required for a SNP to be included (default = 10).

Dynamic Analytical Threshold: The percent of total SNP reads required for a SNP to. be included (default = 0.015 or 1.5%).
A quick note on the ATs: both the static and dynamic ATs are applied and the one producing the higher AT will be used in the EFM software.

Output Folder Name: The name of the folder created within the folder containing the original SNP files to store the generated output for the entire workflow.

Minimum Number of SNPs: The minimum number of SNPs