VCF and PED (optional)-based Variant Filtration

The functionality on this page focuses on utilizing sample information to improve variant quality or to select a subset of samples and variants as needed.

Mutation Type

Option Description Default
--only-snp Only single nucleotide polymorphism (SNP) variants are retained and analyzed.
Format: --only-snp		 [OFF]
--only-indel Only small insertion or deletion (InDel, <=50 bp) variants are retained and analyzed.
Format: --only-indel		 [OFF]

In the following functions, if a PED file is provided, the genotype data for individuals present in both the VCF and PED files will be utilized for the selection process. Without a PED file, the selection will proceed based solely on the genotype data available for all individuals listed in the VCF file.

Allele Frequency

Option Description Default
--local-af Exclude variants in all subjects with alternative allele frequency (AF) outside the range [minAF, maxAF].
Format: --local-af <minAF>~<maxAF>
Example:--local-af 0.05~1.0
Valid setting: [float] 0.0 ~ 1.0		 [OFF]
--local-af-case Exclude variants in cases with alternative allele frequency (AF) outside the range [minAF, maxAF].
Format: --local-af-case <minAF>~<maxAF>
Example:--local-af-case 0.05~1.0
Valid setting: [float] 0.0 ~ 1.0		 [OFF]
--local-af-control Exclude variants in controls with alternative allele frequency (AF) outside the range [minAF, maxAF].
Format: --local-af-control <minAF>~<maxAF>
Example:--local-af-control 0.05~1.0
Valid setting: [float] 0.0 ~ 1.0		 [OFF]
--min-case-control-af-ratio Exclude variants at which the alternative allele frequency (AF) in cases is less than that of in controls multiplied by a specified ratio.
Format: --min-case-control-af-ratio <ratio>
Example:--min-case-control-af-ratio 2.0
Valid setting: [float] >= 0.0		 [OFF]
--local-maf Exclude variants in all subjects with minor allele frequency (MAF) outside the range [minMAF, maxMAF]. By definition, MAF represents the frequency of the less common allele. An interesting thing about the human reference genome is that the “reference” allele is not always the common or “major” allele in the human population. When AF<=0.5, MAF equals AF; when AF > 0.5, MAF is calulated as 1-AF.
Format: --local-maf <minMAF>~<maxMAF>
Example:--local-maf 0.05~0.5
Valid setting: [float] 0.0 ~ 0.5		 [OFF]
--local-maf-case Exclude variants in cases with minor allele frequency (MAF) outside the range [minMAF, maxMAF].
Format: --local-maf-case <minMAF>~<maxMAF>
Example:--local-maf-case 0.05~0.5
Valid setting: [float] 0.0 ~ 0.5		 [OFF]
--local-maf-control Exclude variants in controls with minor allele frequency (MAF) outside the range [minMAF, maxMAF].
Format: --local-maf-control <minMAF>~<maxMAF>
Example:--local-maf-control 0.05~0.5
Valid setting: [float] 0.0 ~ 0.5		 [OFF]
--min-case-control-maf-ratio Exclude variants at which the minor allele frequency (MAF) in cases is less than that of in controls multiplied by a specified ratio.
Format: --min-case-control-maf-ratio <ratio>
Example:--min-case-control-maf-ratio 2.0
Valid setting: [float] >= 0.0		 [OFF]

Missing Genotype Rate

Option Description Default
--min-obs-rate Exclude variants in all subjects with the observed rate of non-missing genotypes <minObsRate.
Format: --min-obs-rate <minObsRate>
Example: --min-obs-rate 0.8
Valid setting: [float] 0.0 ~ 1.0		 [OFF]
--min-obs-rate-case Exclude variants in cases with the observed rate of non-missing genotypes <minObsRate.
Format: --min-obs-rate-case <minObsRate>
Example: --min-obs-rate-case 0.8
Valid setting: [float] 0.0 ~ 1.0		 [OFF]
--min-obs-rate-control Exclude variants in controls with the observed rate of non-missing genotypes <minObsRate.
Format: --min-obs-rate-control <minObsRate>
Example: --min-obs-rate-control 0.8
Valid setting: [float] 0.0 ~ 1.0		 [OFF]

Hardy-Weinberg Equilibrium

Option Description Default
--hwe Exclude variants in all subjects with the Hardy-Weinberg test p value <= pThreshold.
Format: --hwe <pThreshold>
Example: --hwe 1E-5
Valid setting: [double] 0.0 ~ 1.0		 [OFF]
--hwe-case Exclude variants in cases with the Hardy-Weinberg test p value <=pThreshold.
Format: --hwe-case <pThreshold>
Example: --hwe-case 1E-5
Valid setting: [double] 0.0 ~ 1.0		 [OFF]
--hwe-control Exclude variants in controls with the Hardy-Weinberg test p value <=pThreshold.
Format: --hwe-control <pThreshold>
Example: --hwe-control 1E-5
Valid setting: [double] 0.0 ~ 1.0		 [OFF]
Copyright ©MiaoXin Li all right reservedLast modified time: 2025-04-23 08:01:46

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