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Audit Sample QC Fields. #851

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bpblanken opened this issue Jul 26, 2024 · 1 comment
Open

Audit Sample QC Fields. #851

bpblanken opened this issue Jul 26, 2024 · 1 comment
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@bpblanken
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Solicit analyst feedback (some of this has happened already!)

@bpblanken
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bpblanken commented Jul 31, 2024

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.

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