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broadinstitute / seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
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Audit Sample QC Fields. #851

Open bpblanken opened 1 month ago

bpblanken commented 1 month ago

Solicit analyst feedback (some of this has happened already!)

bpblanken commented 1 month ago 
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.