This step must ensure that the pipeline fails early with a descriptive error message when the pheno file contains participants not included in the aggregate vcf.
Can be checked from the VCF header or bcftools query -L or bcftools view my.bcf | awk '/#CHROM/ {print}' | sed 's/\t/\n/g' | head -30
This step must ensure that the pipeline fails early with a descriptive error message when the pheno file contains participants not included in the aggregate vcf.
Can be checked from the VCF header or
bcftools query -Lorbcftools view my.bcf | awk '/#CHROM/ {print}' | sed 's/\t/\n/g' | head -30