Question: genotypeToSnpMatrix doesn't handle PL
gravatar for TimothéeFlutre
4.1 years ago by
TimothéeFlutre70 wrote:

I would like to convert possibly-uncertain genotypes from a VCF to a snpMatrix object. My VCF file was produced by GATK 3.4-46 and complies with VCF specification 4.1. Here is what I am doing:

vcf <- readVcf(file=tabix.file, genome="test", param=vcf.params)
snp.mat <- genotypeToSnpMatrix(vcf, uncertain=TRUE)
In .local(x, ...) : uncertain=TRUE requires GP or GL; returning NULL

Could it be possible to add support for PL (phred-scaled genotype likelihood) ?

Here is my sessionInfo():

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] snpStats_1.20.0 Matrix_1.2-2
[3] survival_2.38-3 VariantAnnotation_1.16.0
[5] Rsamtools_1.22.0 Biostrings_2.38.0
[7] XVector_0.10.0 SummarizedExperiment_1.0.0
[9] Biobase_2.30.0 GenomicRanges_1.22.0
[11] GenomeInfoDb_1.6.0 IRanges_2.4.0
[13] S4Vectors_0.8.0 BiocGenerics_0.16.0


variantannotation vcf • 562 views
ADD COMMENTlink modified 4.0 years ago by Stephanie M. Gogarten740 • written 4.1 years ago by TimothéeFlutre70

Adding PL to genotypeToSnpMatrix has been lurking on the bottom of my to-do list for probably a couple of years now. Time to move it to the top. I will try to get it done in the next week or two.

ADD REPLYlink written 4.1 years ago by Stephanie M. Gogarten740

That would be great! I'll make sure to check this page regularly then.

ADD REPLYlink written 4.1 years ago by TimothéeFlutre70
Answer: genotypeToSnpMatrix doesn't handle PL
gravatar for Stephanie M. Gogarten
4.0 years ago by
University of Washington
Stephanie M. Gogarten740 wrote:

VariantAnnotation 1.17.8 adds support for the PL field. It should be available later today after propagating through the build process.

ADD COMMENTlink written 4.0 years ago by Stephanie M. Gogarten740
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