filter_flags
# Sets "filter_flags" on Individual
# List of strings on the left, pulls value from flag on the right.
'callrate': 'filtered_callrate',
'contamination': 'PCT_CONTAMINATION',
'chimera': 'AL_PCT_CHIMERAS',
'coverage_exome': 'HS_PCT_TARGET_BASES_20X',
'coverage_genome': 'WGS_MEAN_COVERAGE'
pop_platform_filters
# Sets pop_platform_filters on Individual
sample_qc.*
qc_pop
# Sets population on Individual
e.g. SAS, AMR
qc_platform
# Unused
e.g. Standard Germline Exome v5
pop_PC1 pop_PC2 pop_PC3 pop_PC4 pop_PC5 pop_PC6
# I don't think these are used.