Create workflow specs for QC of genotype array data

[ngaddis]

Overview of process:

• Starting point: PLINK format, PLUS strand GRCh37
• Convert variants to IMPUTE2 ID format
• Remove duplicate IDs (based on call rate)
• Flag individuals missing chrX or other chromosome
• Remove phenotype info in FAM file
• Format phenotype data to standard format
• Structure workflow (Create workflow specs for STRUCTURE (QC sub-workflow) #4)
• Partition data by ancestry
• Call rate filter
• HWE filter
• Subject call rate filter (based on autosomes)
• Relatedness workflow (Create workflow specs for relatedness filtering (QC sub-workflow) #5)
• Remove samples based on relatedness
• Sex check and sample removal
• Excessive homozygosity filtering
• Set het haploids to missing