filtervcf: Filter variants with user-specified quality criteria
In VPA: Variant Pattern Analyzer for next-generation sequencing study

Description Usage Arguments Value Author(s) See Also Examples

VCF format file contains various score to assess the positional-level quality of variant and sequence call. The function filtervcf can be used to filter variants with user-specified quality criteria.

1 2	filtervcf(vcf, alter = NULL, alter.PL=20, alter.AD=3, alter.ADP=NULL, QUAL = 20, DP = c(10,500), GQ = NULL, FILTER = NULL, INDEL = NULL)

`vcf`	A VCF object for filtering.
`alter`	Logical value. If TRUE, the variant positions are kept. If FALSE, the variant positions are discarded. If NULL, the option will be ignored.
`alter.PL`	Phred-scaled genotype likelihoods of variant call to define a variant. The PL information can be extracted from PL column (both GATK and Samtools) in the VCF data.
`alter.AD`	The minimum depth of variant allele when alter is TRUE. The information of variant allele depth can be extracted from AD (GATK) or DP4 (Samtools) column in the VCF data.
`alter.ADP`	The minimum percentage of read depth containing variant allele.
`QUAL`	phred-scaled variant likelihoods of variant call. The QUAL information can be extracted from QUAL column (both GATK and Samtools) in the VCF data.
`DP`	The minimum and maximum of position-level read depth. The DP information can be extracted from DP column (both GATK and Samtools) in the VCF data.
`GQ`	Phred-scaled score for most likely genotype at position of interest. The GQ information can be extracted from GQ column (both GATK and Samtools) in the VCF data. If NULL, the option will be ignored.
`FILTER`	'NULL' or 'PASS'. The VCF format of variant call produced by GATK will label quality status of each position. This information can be extracted from FILTER column (GATK) in the VCF data. If the VCF data is produced by Samtools, FILTER column will contain empty information. If 'NULL' is set, all variants will be parsed. If 'PASS' is set, only variant with 'PASS' label will be parsed.
`INDEL`	Logical value. If TRUE, only INDELs are evaluated. If FALSE, only point variants are evaluated. If NULL, the option will be ignored.

The input vcf data will be filtered by user-specified quality criteria. A list including filtered vcf data and dropped vcf data will return.

Qiang Hu

subvcf

#Filter alignment artifacts to get promising SNP
#vcffile <- system.file("extdata", "1151HZ0001.flt.vcf", package="VPA")
#vcfdata <- read.vcf(vcffile)
#vcflt <- filtervcf(vcfdata, alter=TRUE, alter.AD=3, QUAL=20,
#DP=c(10,500), GQ=20, INDEL=FALSE)$filtered
#write.vcf(vcflt)