Question: intansv - problem reading vcf output from delly ver 0.6.7
gravatar for rajini28m
4.0 years ago by
United States
rajini28m0 wrote:

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)

[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 • 601 views
ADD COMMENTlink modified 2.3 years ago by morovatunc0 • written 4.0 years ago by rajini28m0
Answer: intansv - problem reading vcf output from delly ver 0.6.7
gravatar for morovatunc
2.3 years ago by
morovatunc0 wrote:

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



ADD COMMENTlink written 2.3 years ago by morovatunc0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 188 users visited in the last hour