Closed lsantuari closed 5 years ago
A clean install of R 3.6.1 with the following script:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("StructuralVariantAnnotation")
library(StructuralVariantAnnotation)
vcf = readVcf("C:\\Users\\Daniel\\Downloads/CHM1_CHM13_pseudodiploid_SVs.vcf")
gr = breakpointRanges(vcf)
Gives the following output:
Warning message:
In .breakpointRanges(x, ...) :
Found 9 duplicate row names (duplicates renamed).
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] StructuralVariantAnnotation_1.0.0 VariantAnnotation_1.30.1
[3] Rsamtools_2.0.0 Biostrings_2.52.0
[5] XVector_0.24.0 SummarizedExperiment_1.14.1
[7] DelayedArray_0.10.0 BiocParallel_1.18.0
[9] matrixStats_0.54.0 Biobase_2.44.0
[11] rtracklayer_1.44.2 GenomicRanges_1.36.0
[13] GenomeInfoDb_1.20.0 IRanges_2.18.1
[15] S4Vectors_0.22.0 BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 compiler_3.6.1 pillar_1.4.2
[4] BiocManager_1.30.4 prettyunits_1.0.2 progress_1.2.2
[7] GenomicFeatures_1.36.4 bitops_1.0-6 tools_3.6.1
[10] zlibbioc_1.30.0 biomaRt_2.40.3 digest_0.6.20
[13] zeallot_0.1.0 bit_1.1-14 BSgenome_1.52.0
[16] memoise_1.1.0 RSQLite_2.1.2 tibble_2.1.3
[19] lattice_0.20-38 pkgconfig_2.0.2 rlang_0.4.0
[22] Matrix_1.2-17 DBI_1.0.0 GenomeInfoDbData_1.2.1
[25] dplyr_0.8.3 httr_1.4.0 stringr_1.4.0
[28] hms_0.5.0 vctrs_0.2.0 tidyselect_0.2.5
[31] bit64_0.9-7 grid_3.6.1 glue_1.3.1
[34] R6_2.4.0 AnnotationDbi_1.46.0 XML_3.98-1.20
[37] purrr_0.3.2 magrittr_1.5 blob_1.2.0
[40] backports_1.1.4 GenomicAlignments_1.20.1 assertthat_0.2.1
[43] stringi_1.4.3 RCurl_1.95-4.12 crayon_1.3.4
You might have a old version that doesn't have this bug fixed https://github.com/Bioconductor/VariantAnnotation/issues/19
Hi Daniel,
The file "CHM1_CHM13_pseudodiploid_SVs.vcf" works fine for me. However, the files "CHM1_SVs.annotated.vcf.gz" and "CHM13_SVs.annotated.vcf.gz" trigger the "Unrecognised format" error. Do they work for you?
>sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.2.0 dplyr_0.8.3 StructuralVariantAnnotation_1.1.0
[4] VariantAnnotation_1.31.3 Rsamtools_2.1.3 Biostrings_2.53.1
[7] XVector_0.25.0 SummarizedExperiment_1.15.5 DelayedArray_0.11.4
[10] BiocParallel_1.19.0 matrixStats_0.54.0 Biobase_2.45.0
[13] rtracklayer_1.45.1 GenomicRanges_1.37.14 GenomeInfoDb_1.21.1
[16] IRanges_2.19.10 S4Vectors_0.23.17 BiocGenerics_0.31.5
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 lattice_0.20-38 prettyunits_1.0.2 assertthat_0.2.1 digest_0.6.20
[6] BiocFileCache_1.9.1 R6_2.4.0 RSQLite_2.1.1 httr_1.4.0 pillar_1.4.2
[11] zlibbioc_1.31.0 rlang_0.4.0 GenomicFeatures_1.37.3 progress_1.2.2 lazyeval_0.2.2
[16] curl_3.3 rstudioapi_0.10 blob_1.1.1 Matrix_1.2-17 labeling_0.3
[21] stringr_1.4.0 RCurl_1.95-4.12 bit_1.1-14 biomaRt_2.41.6 munsell_0.5.0
[26] compiler_3.6.1 pkgconfig_2.0.2 askpass_1.1 openssl_1.4 tidyselect_0.2.5
[31] tibble_2.1.3 GenomeInfoDbData_1.2.1 XML_3.98-1.20 withr_2.1.2 crayon_1.3.4
[36] dbplyr_1.4.2 GenomicAlignments_1.21.4 bitops_1.0-6 rappdirs_0.3.1 grid_3.6.1
[41] gtable_0.3.0 DBI_1.0.0 magrittr_1.5 scales_1.0.0 stringi_1.4.3
[46] tools_3.6.1 bit64_0.9-7 BSgenome_1.53.0 glue_1.3.1 purrr_0.3.2
[51] hms_0.4.2 AnnotationDbi_1.47.0 colorspace_1.4-1 BiocManager_1.30.4 memoise_1.1.0
However, the files "CHM1_SVs.annotated.vcf.gz" and "CHM13_SVs.annotated.vcf.gz" trigger the "Unrecognised format" error. Do they work for you?
They do not work for me because they are malformed VCFs that do not conform to the specifications. The issue is with the SVTYPE field and if you search/replace their custom definitions (e.g. SVTYPE=insertion
) with the spec-defined values (e.g. SVTYPE=INS
) they work fine.
Hello,
When I try to load the truth sets (VCF files) from the Huddleston2016 dataset I get the following error (for instance for CHM1):
Thank you in advance for the support.
Cheers, Luca