Quality Control

Quality control is split into local sample filtering and global SNP filtering.

Local QC

exclude_samples_by_missing_rate runs PLINK --mind to remove samples whose missing genotype rate exceeds the configured threshold:

plink --bfile <plink_prefix> --mind <threshold> --make-bed --out <new_prefix>

The output prefix is written under the center's configured output.log_dir, and the client updates its active plink_prefix.

Global QC

During global_qc, each client computes:

• Genotype counts and HWE values with compute_genotype_counts, using plink --freq and plink --hardy.
• SNP missingness counts with compute_missingness_counts, using plink --missing.
• Threshold arrays containing MAF, missingness, and HWE thresholds.

Clients pack these arrays as typed payloads and encrypt them for peers. The server forwards the ciphertext arrays during global_qc; it does not compute the exclusion list.

During global_qc_response, each client decrypts peer payloads and _compute_exclusion_list then:

1. Sums all genotype and missingness arrays.
2. Derives unified thresholds from all clients.
3. Computes MAF, missingness rate, and HWE chi-square p-values for each SNP.
4. Returns the SNP IDs that should be excluded locally.

SNP filtering

Clients apply the returned exclusion list with exclude_snps:

plink --bfile <plink_prefix> --exclude <exclude_file> --make-bed --out <new_prefix>

If the exclusion list is empty, the original plink_prefix is kept.