QV builder

Build a QV YAML by adding statement lines in a simple key=value format (quote values with spaces). Use meta for set info, filters and criteria for rules, and optional notes. The preview shows the structured YAML.

Examples

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meta qv_set_id="qv_gwas_common_v1_20250827"

meta version="1.0.0"

meta title="GWAS common QC"

meta description="Common GWAS criteria expressed in tool-agnostic form"

meta created="2025-08-27"

meta authors=Alice,Bob

meta tags=GWAS,QC,PCA

note "implementations are hints only"

filter maf_minimum field=MAF operator=">=" value=0.01 desc="Minimum MAF"

filter hwe field=HWE_P operator=">=" value=1e-6 logic=keep_if

criteria pm2 field=gnomAD_AF operator="<" value=1e-6 logic=and desc="Absent or rare"

criteria ps5 field=IMPACT operator="==" value=HIGH desc="Comp het with HIGH"

criteria ps5 group_by=sample,SYMBOL count=">=2"

filter region_include desc="include panel" field=OVERLAP(targets.exome.bed) operator=">=" value=1 logic=keep_if

criteria disease_panel logic=and desc="HIGH impact within panel"
criteria disease_panel field=IMPACT operator="==" value=HIGH
criteria disease_panel field=OVERLAP(targets.exome.bed) operator=">=" value=1

meta description_patient="There is a strong family history of early heart attacks. I would like clear information on any inherited cardiac risk and what I can do next."

meta description_ppie="The PPIE working group reviewed the qualifying criteria and approved the final protocol on 2025-08-15."

criteria ACMG_PVS1 logic=and description="Null variants (IMPACT == HIGH) in genes where loss of function causes disease. Includes homozygous variants, compound heterozygous cases, or dominant inheritance. Warning to phase check compound heterozygosity."
        criteria ACMG_PVS1 field=IMPACT operator="==" value=HIGH
        criteria ACMG_PVS1 group=any_of:start
        criteria ACMG_PVS1 field=genotype operator="==" value=2
        criteria ACMG_PVS1 field=Inheritance operator="==" value=AD
        criteria ACMG_PVS1 field=comp_het_flag operator="==" value=1
        criteria ACMG_PVS1 group=any_of:end

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