VCF-based Quality Control

Genotype-level Quality Control

Removing genotypes if at least one of the options is set to true.

Option	Description	Default
`--gty-gq`	Exclude genotypes with the minimal genotype quality (Phred Quality Score) per genotype < `minGq`. Set to '0' to disable this filter. Format: `--gty-gq <minGq>` Example: `--gty-gq 20` Valid setting: [int] >=0	20
`--gty-dp`	Exclude genotypes with the minimal read depth per genotype < `minDp`. Set to '0' to disable this filter. Format: `--gty-dp <minDp>` Example: `--gty-dp 8` Valid setting: [int] >=0	8
`--gty-pl`	Exclude genotypes with the second smallest normalized Phred-scaled likelihoods for genotypes < `minPl`. Otherwise, there would be confusing genotypes. Set to '0' to disable this filter. Format: `--gty-pl <minPl>` Example: `--gty-pl 20` Valid setting: [int]>=0	20
`--gty-ad-hom-ref`	Exclude genotypes with the fraction of the reads carrying alternative allele > `maxAdHomRef` at a reference-allele homozygous genotype. Set to '1' to disable this filter. Format: `--gty-ad-hom-ref <maxAdHomRef>` Example: `--gty-ad-hom-ref 0.05` Valid setting: [float] 0.0 ~ 1.0	0.05
`--gty-ad-hom-alt`	Exclude genotypes with the fraction of the reads carrying alternative allele < `minAdHomAlt` at an alternative-allele homozygous genotype. Set to '0' to disable this filter. Format: `--gty-ad-hom-alt <minAdHomAlt>` Example: `--gty-ad-hom-alt 0.75` Valid setting: [float] 0.0 ~ 1.0	0.75
`--gty-ad-het`	Exclude genotypes with the fraction of the reads carrying alternative allele < `minAdHet` at a heterozygous genotype. Set to '0' to disable this filter. Format: `--gty-ad-het <minAdHet>` Example: `--gty-ad-het 0.25` Valid setting: [float] 0.0 ~ 1.0	0.25
`--gty-qc`	Exclude genotypes where the genotype quality metric corresponding to the `keyword` has not passed Java expression quality control. `--gty-qc`is is a combination of parameters that meet custom genotype QC needs. The `default` tag is used to control whether to retain or discard the genotype when a quality control parsing error occurs. Format: `--gty-qc <keyword> <rule> default=[RETAIN/DISCARD]` Example: `--gty-qc DP "DP.toInt()>=10" default=DISCARD`	[OFF]

Variant-level Quality Control

Option	Description	Default
`--allele-num`	Exclude variants with the alternative allele number per variant outside the range [`minAlleleNum`, `maxAlleleNum`]. Format: `--allele-num <minAlleleNum>~<maxAlleleNum>` Example: `--allele-num 2~4` Valid setting: [int] 0 ~ 255	[OFF]
`--seq-ac`	Exclude variants with the alternative allele count (AC) per variant outside the range [`minAc`, `maxAc`]. Format: `--seq-ac <minAc>~<maxAc>` Example: `--seq-ac 1~10` Valid setting: [int] >=0	[OFF]
`--seq-an`	Exclude variants with the non-missing allele number (AN) per variant outside the range [`minAn`, `maxAn`]. Format: `--seq-an <minAn>~<maxAn>` Example: `--seq-an 160~200` Valid setting: [int] >=0	[OFF]
`--seq-af`	Exclude variants with the alternative allele frequency (AF) per variant outside the range [`minAf`, `maxAf`]. Format: `--seq-af <minAf>~<maxAf>` Example: `--seq-af 0.05~1.0` Valid setting: [float] 0.0 ~ 1.0	[OFF]
`--seq-qual`	Exclude variants with the minimal overall sequencing quality score (Phred Quality Score) per variant < `minQual`. Format: `--seq-qual <minQual>` Example: `--seq-qual 30` Valid setting: [float] >=0.0	30
`--seq-mq`	Exclude variants with the minimal overall mapping quality score (Mapping Quality Score) per variant < `minMq`. Format: `--seq-mq <minMq>` Example: `--seq-mq 20` Valid setting: [float] >=0.0	20
`--seq-fs`	Exclude variants with the overall strand bias Phred-scaled p-value (using Fisher's exact test) per variant > `maxFs`. The strand bias estimation is best suited for low-coverage situations. Set to '100' to disable this filter as the maximal phred-scaled p-value is 100. Format: `--seq-fs <maxFs>` Example: `--seq-fs 60` Valid setting: [float] >=0.0	100
`--seq-info`	Exclude variants where the value of the specified `keyword` in the INFO field does not pass the Java expression quality control. `--seq-info`is a combination of parameters. The `default` tag is used to control whether to retain or discard the genotype when a quality control parsing error occurs. Format: `--seq-info <keyword> <rule> default=[RETAIN/DISCARD]` Example: `--seq-info keyword=MQ rule=MQ.char2Float()>=20 default=DISCARD`	[OFF]
`--seq-filter`	Exclude variants where the value of the specified keyword in the FILTER field of VCF does not pass quality control. It uses Java expressions flexibly. In the expressions, e.g., 'value.XXX(string)' operates the value of the FILTER field as a Java String. Format: `--seq-filter Java String expression` Example: `--seq-filter value.valueEquals(\"PASS\")` will exclude variants at which the FILTER field is not equal to PASS --seq-filter value.indexOf(\"q10\") != -1` will exclude variants at which the FILTER field contains q10	[OFF]

Turn Off Quality Control

All quality control options mentioned above, including genotype-level and variant-level quality control options, can be turned off by --disable-qc.

Option	Description	Default
`--disable-qc`	Disable all quality control options mentioned above. NOTE It cannot be used in conjunction with other quality control options, as it will render them ineffective. Format: `--disable-qc`	[OFF]

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