Question: VCF files incompatible with signeR
0
gravatar for Dan
6 months ago by
Dan0
Dan0 wrote:

I'm trying to analyze VCF files generated by the Qiagen CLC Genomics Workbench using signeR to detect mutation signatures, and signeR does not like the format of the VCF files for some reason. This is a small panel of targets (12 loci across 4 chromosomes in human samples).

Here is the following code and error message that I get:

library(signeR) library(VariantAnnotation) library(BSgenome.Hsapiens.UCSC.hg19) vcfobj <- readVcf("D:\R\Sample17.NT.vcf", "hg19")

library(Rsamtools) mygenome <- FaFile("D:\R\Homosapienshg19_sequence.fa") mut <- genCountMatrixFromVcf(mygenome, vcfobj) Error in attributes(.Data) <- c(attributes(.Data), attrib) : dims [product 10] do not match the length of object [20]

I'm pretty new with using R, so I'm having trouble interpreting the error message. Does anyone know of any good ways to identify and resolve the issue?

Thanks

software error signer • 149 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by Dan0
Answer: VCF files incompatible with signeR
0
gravatar for Dan
6 months ago by
Dan0
Dan0 wrote:

I think I may have figured it out; signeR doesn't like VCF files that have variants greater than 1 base. I generated a VCF file that only included single base changes and that worked.

ADD COMMENTlink written 6 months ago by Dan0

Hello Dan, thats weird signeR uses VariantAnnotation::isSNV to filter out indels, if you could send me an example of a vcf file with the issue I could look into it better.

ADD REPLYlink written 6 months ago by renan.valieris10
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