intansv - problem reading vcf output from delly ver 0.6.7
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rajini28m • 0
@rajini28m-8572
Last seen 6.2 years ago
United States

I am getting this error when i try to read the vcf output from Delly ver 0.6.7

Error in dellyCont[dellyCont$map_quality >= minMappingQuality & dellyCont$rp_support >=  :
  incorrect number of dimensions

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.28.6   intansv_1.8.0        GenomicRanges_1.20.5 GenomeInfoDb_1.4.1   IRanges_2.2.5       
 [6] S4Vectors_0.6.3      plyr_1.8.3           ggbio_1.16.1         BiocGenerics_0.14.0  ggplot2_1.0.1       

loaded via a namespace (and not attached):
 [1] VariantAnnotation_1.14.6 reshape2_1.4.1           splines_3.2.1            lattice_0.20-33         
 [5] colorspace_1.2-6         GenomicFeatures_1.20.1   RBGL_1.44.0              survival_2.38-3         
 [9] XML_3.98-1.3             foreign_0.8-65           DBI_0.3.1                BiocParallel_1.2.18     
[13] RColorBrewer_1.1-2       lambda.r_1.1.7           stringr_1.0.0            zlibbioc_1.14.0         
[17] Biostrings_2.36.2        munsell_0.4.2            gtable_0.1.2             futile.logger_1.4.1     
[21] OrganismDbi_1.10.0       latticeExtra_0.6-26      Biobase_2.28.0           GGally_0.5.0            
[25] biomaRt_2.24.0           AnnotationDbi_1.30.1     proto_0.3-10             Rcpp_0.12.0             
[29] acepack_1.3-3.3          BSgenome_1.36.3          scales_0.2.5             graph_1.46.0            
[33] Hmisc_3.16-0             XVector_0.8.0            Rsamtools_1.20.4         gridExtra_2.0.0         
[37] digest_0.6.8             stringi_0.5-5            biovizBase_1.16.0        grid_3.2.1              
[41] tools_3.2.1              bitops_1.0-6             magrittr_1.5             RCurl_1.95-4.7          
[45] RSQLite_1.0.0            dichromat_2.0-0          Formula_1.2-1            cluster_2.0.3           
[49] futile.options_1.0.0     MASS_7.3-43              reshape_0.8.5            rpart_4.1-10            
[53] GenomicAlignments_1.4.1  nnet_7.3-10

intansv • 746 views
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morovatunc • 0
@morovatunc-12812
Last seen 4.5 years ago

I am having the exact problem. have you found any solution ?

Thanks

 

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