filterVcfBasic {PureCN} | R Documentation

## Basic VCF filter function

### Description

Function to remove artifacts and low confidence/quality variant calls.

### Usage

    filterVcfBasic(vcf, tumor.id.in.vcf = NULL, use.somatic.status = TRUE,
      snp.blacklist = NULL, af.range = c(0.03, 0.97),
      contamination.range = c(0.01, 0.075), min.coverage = 15,
      min.base.quality = 25, min.supporting.reads = NULL, error = 0.001,
      target.granges = NULL, remove.off.target.snvs = TRUE,
      model.homozygous = FALSE, interval.padding = 50, DB.info.flag = "DB")

### Arguments

`vcf` | `CollapsedVCF` object, read in with the `readVcf` function from the VariantAnnotation package.
`tumor.id.in.vcf` | The tumor id in the `CollapsedVCF` (optional).
`use.somatic.status` | If somatic status and germline data is available, then use this information to remove non-heterozygous germline SNPs or germline SNPS with biased allelic fractions.
`snp.blacklist` | A file with blacklisted genomic regions. Must be parsable by `import` from `rtracklayer`, for a example a BED file with file extension ‘.bed’.
`af.range` | Exclude variants with allelic fraction smaller or greater than the two values, respectively. The higher value removes homozygous SNPs, which potentially have allelic fractions smaller than 1 due to artifacts or contamination. If a matched normal is available, this value is ignored, because homozygosity can be confirmed in the normal.
`contamination.range` | Count variants in dbSNP with allelic fraction in the specified range. If the number of these putative contamination variants exceeds an expected value and if they are found on almost all chromosomes, the sample is flagged as potentially contaminated and extra contamination estimation steps will be performed later on.
`min.coverage` | Minimum coverage in tumor. Variants with lower coverage are ignored.
`min.base.quality` | Minimim base quality in tumor. Requires a `BQ` genotype field in the VCF.
`min.supporting.reads` | Minimum number of reads supporting the alt allele. If `NULL`, calculate based on coverage and assuming sequencing error of 10^-3.
`error` | Estimated sequencing error rate. Used to calculate minimum number of supporting reads using `calculatePowerDetectSomatic`.
`target.granges` | `GenomicRanges` object specifiying the target postions. Used to remove off-target reads. If `NULL`, do not check whether variants are on or off-target.
`remove.off.target.snvs` | If set to a true value, will remove all SNVs outside the covered regions.
`model.homozygous` | If set to `TRUE`, does not remove homozygous variants. Ignored in case a matched normal is provided in the VCF.
`interval.padding` | Include variants in the interval flanking regions of the specified size in bp. Requires `target.granges`.
`DB.info.flag` | Flag in INFO of VCF that marks presence in common germline databases. Defaults to `DB` that may contain somatic variants if it is from an unfiltered dbSNP VCF.

### Value

A list with elements

`vcf` | The filtered `CollapsedVCF` object.
`flag` | A flag (`logical(1)`) if problems were identified.
`flag_comment` | A comment describing the flagging.

### Author(s)

Markus Riester

### See Also

`calculatePowerDetectSomatic`

### Examples

    # This function is typically only called by runAbsolute via
    # fun.filterVcf and args.filterVcf.
    vcf.file <- system.file("extdata", "example_vcf.vcf.gz", package="PureCN")
    vcf <- readVcf(vcf.file, "hg19")
    vcf.filtered <- filterVcfBasic(vcf)

[Package PureCN version 1.10.0 Index]