Hello,

I would like to filter one vcf by selecting only SNVs and in addition, those that only match genomic coordinates of a provided GRanges. I know that the filterVcf() function of Variant Annotation can deal with those requirements by using the isSNV() function on filters and by selecting on param argument the ScanVcfParam option. However, when just selecting the SNV filter I got some message errors and I do not know how to proceed. I've been following the Bioconductor tutorial <http://bioconductor.org/help/course-materials/2014/BioC2014/Lawrence_Tutorial.R>, but still I don't know what is the error with extractROWS.

I use the chr7 default vcf in the extdata folder of the package in order to show you my problem.

> library(VariantAnnotation)

> fl <- system.file("extdata", "chr7-sub.vcf.gz", package="VariantAnnotation")
> destination.file <- "~/destination.vcf"

> filterVcf(fl,
+           "hg19",
+           destination.file,
+           filters=FilterRules(list(onlySNV=isSNV)),
+           verbose=TRUE)
starting filter
filtering 3791 records
Error in extractROWS(x, eval(filter, x)) :
  error in evaluating the argument 'i' in selecting a method for function 'extractROWS': Error in rule(envir) :
  call to standardGeneric("isSNV") apparently not from the body of that generic function

May I pass the isSNV function in another way?

I would appreciate you opinion.

Thank you very much,

Pau.

This is fixed in release (IRanges 2.2.6) and devel (S4Vectors). Will take some time to propagate.

Thanks Michael!! With the update now seems that the isSNV argument is working perfectly!

However, I'm just stacked again with this function. My goal by using this function is also to filter both with the SNVs and also by specifying genomic coordinates with the param argument using the ScanVcfParam. However, when I pass a GRanges to this function, like is done in the tutorial mentioned in the previous message, it raises an error of the writeVcf function. However, when I do a test using the function with readVcf() and specifying the same param, it seems that everything goes smoothly. May I be doing something wrong?

>library(VariantAnnotation)
>library(TxDb.Hsapiens.UCSC.hg19.knownGene)

> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> exons_by_gene <- exonsBy(txdb,"gene")
> exons_by_gene <- resize(exons_by_gene, width(exons_by_gene)+101, fix="start", use.names=TRUE, ignore.strand=FALSE)
> exons_by_gene <- resize(exons_by_gene, width(exons_by_gene)+101, fix="end", use.names=TRUE, ignore.strand=FALSE)
> exons_by_gene2 <- unlist(exons_by_gene)
> exons_by_gene2 <- exons_by_gene2[seqnames(exons_by_gene2)=="chr22"]
> seqlevelsStyle(exons_by_gene2) <- "NCBI"
>
> fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> destination.file <-"~/destination.vcf"
>
> filterVcf(fl,
+           "hg19",
+           destination.file,
+           filters=FilterRules(list(onlySNV=isSNV)),
+           verbose=TRUE,
+           param=ScanVcfParam(which=exons_by_gene2))
starting filter
found header lines for 3 ‘fixed’ fields: ALT, QUAL, FILTER
found header lines for 22 ‘info’ fields: LDAF, AVGPOST, ..., VT, SNPSOURCE
found header lines for 3 ‘geno’ fields: GT, DS, GL
filtering 3594 records
Error in writeVcf(vcfChunk, filtered) :
  error in evaluating the argument 'filename' in selecting a method for function 'writeVcf': Error: object 'filtered' not found


test <- readVcf(fl, "hg19", destination.file, param=ScanVcfParam(which=exons_by_gene2))

Thanks in advance.

Pau