read_vcfs_as_granges() does not work

[CPTPaso]

Hi,

I am trying to run the code from the R vignette. However

grl <- read_vcfs_as_granges(vcf_files, sample_names, ref_genome)

throws the error "Some of your data is missing a ALT column." I run the code exactly as it is given in the vignette and also use the vcf files of the package. I also checked these files and there definitely is an ALT column.

How can I fix this?

[FreekManders]

Hi,

This should work. Can you share your session info and the code you have run?

[CPTPaso]

Sure!

SessionInfo: R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.58.0
[3] rtracklayer_1.49.5 Biostrings_2.57.2
[5] XVector_0.29.3 MutationalPatterns_3.0.1
[7] NMF_0.23.0 Biobase_2.49.1
[9] cluster_2.1.0 rngtools_1.5
[11] pkgmaker_0.32.2 registry_0.5-1
[13] GenomicRanges_1.42.0 GenomeInfoDb_1.25.11
[15] IRanges_2.23.10 S4Vectors_0.27.12
[17] BiocGenerics_0.35.4 ggplot2_3.3.2

loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.57.0 bit64_4.0.5
[4] doParallel_1.0.15 RColorBrewer_1.1-2 progress_1.2.2
[7] httr_1.4.2 tools_4.0.2 R6_2.4.1
[10] DBI_1.1.0 colorspace_1.4-1 withr_2.2.0
[13] tidyselect_1.1.0 prettyunits_1.1.1 curl_4.3
[16] bit_4.0.4 compiler_4.0.2 xml2_1.3.2
[19] DelayedArray_0.15.7 scales_1.1.1 askpass_1.1
[22] rappdirs_0.3.1 stringr_1.4.0 digest_0.6.25
[25] Rsamtools_2.5.3 rmarkdown_2.3 pkgconfig_2.0.3
[28] htmltools_0.5.0 MatrixGenerics_1.2.0 dbplyr_1.4.4
[31] rlang_0.4.7 rstudioapi_0.11 RSQLite_2.2.0
[34] generics_0.0.2 BiocParallel_1.23.2 dplyr_1.0.2
[37] VariantAnnotation_1.36.0 RCurl_1.98-1.2 magrittr_1.5
[40] GenomeInfoDbData_1.2.3 Matrix_1.2-18 Rcpp_1.0.5
[43] munsell_0.5.0 lifecycle_0.2.0 stringi_1.4.6
[46] yaml_2.2.1 ggalluvial_0.12.3 SummarizedExperiment_1.19.6 [49] zlibbioc_1.34.0 plyr_1.8.6 BiocFileCache_1.13.1
[52] grid_4.0.2 blob_1.2.1 crayon_1.3.4
[55] lattice_0.20-41 GenomicFeatures_1.40.1 hms_0.5.3
[58] knitr_1.29 pillar_1.4.6 reshape2_1.4.4
[61] codetools_0.2-16 biomaRt_2.46.0 XML_3.99-0.5
[64] glue_1.4.1 evaluate_0.14 BiocManager_1.30.10
[67] vctrs_0.3.2 foreach_1.5.0 gtable_0.3.0
[70] openssl_1.4.2 purrr_0.3.4 assertthat_0.2.1
[73] xfun_0.16 gridBase_0.4-7 xtable_1.8-4
[76] pracma_2.3.3 tibble_3.0.3 iterators_1.0.12
[79] GenomicAlignments_1.25.3 AnnotationDbi_1.51.3 memoise_1.1.0
[82] ellipsis_0.3.1

Code:

----setup, include=FALSE-----------------------------------------------------

knitr::opts_chunk$set(echo = TRUE)

---- echo=FALSE------------------------------------------------------------------------------

options(width = 96) library(ggplot2) library(BiocStyle)

----install_package, eval=FALSE--------------------------------------------------------------

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("MutationalPatterns")

----Load package, message=FALSE--------------------------------------------------------------

library(MutationalPatterns)

---- message=FALSE---------------------------------------------------------------------------

library(BSgenome) head(available.genomes())

---------------------------------------------------------------------------------------------

ref_genome <- "BSgenome.Hsapiens.UCSC.hg19" library(ref_genome, character.only = TRUE)

----locate_vcfs------------------------------------------------------------------------------

vcf_files <- list.files(system.file("extdata", package = "MutationalPatterns"), pattern = "sample.vcf", full.names = TRUE )

vcf_files <- vcf_files[2]

----set_sample_names-------------------------------------------------------------------------

sample_names <- "colon2"

----read_vcfs_as_granges, message=FALSE------------------------------------------------------

grl <- read_vcfs_as_granges(vcf_files, sample_names, ref_genome)

sessionInfo()

[FreekManders]

Running the same code on my machine doesn't generate an error. What happens if you try to run GenomicRanges:granges(VariantAnnotation::readVcf(vcf_files))? Does this generate a granges object with an ALT column?

[CPTPaso]

When I run GenomicRanges::granges(VariantAnnotation::readVcf(vcf_files)) I still get a granges object with only seqnames, start, end, width, strand, paramRangeID and an ID like 1:105605108_T/A as rownames.

Now, I try and transform that granges object into a dataframe, dissect the rownames, extract REF and ALT, generate a new dataframe including REF and ALT and use makeGRangesFromDataFrame() to generate a new granges object. That could do the trick. But that's circumstancial.

Do you have an idea why granges does not recognize the ALT and REF col in the vcf files?

[CPTPaso]

The problem was on my end. I ran mutational Patterns on another PC which worked without any error. So there has to be something about my R environment. But this is something I can figure out. Thanks anyhow for your help!