In a low-depth bcftools caller test, the raw VCF was generated successfully with 4 samples, but QC later failed in PLINK because modules.qc.min_depth: 2 filtered out every sample.
Observed depths were all below the threshold:
SAMEA6426319 0.634927
SAMEA6426320 0.643195
SAMEA6426321 0.555313
SAMEA6426322 0.569276
This left results/qc/individuals.samps.txt empty. qc_subsample_snps then created 0-sample VCFs, and PLINK failed with:
Error: No samples in --vcf file.
Expected behavior: if QC filtering removes all samples, fail immediately with a clear error saying which filter removed them and suggesting adjusting modules.qc.min_depth for low-depth/downsampled tests.
In a low-depth bcftools caller test, the raw VCF was generated successfully with 4 samples, but QC later failed in PLINK because
modules.qc.min_depth: 2filtered out every sample.Observed depths were all below the threshold:
This left results/qc/individuals.samps.txt empty. qc_subsample_snps then created 0-sample VCFs, and PLINK failed with:
Expected behavior: if QC filtering removes all samples, fail immediately with a clear error saying which filter removed them and suggesting adjusting modules.qc.min_depth for low-depth/downsampled tests.