intansv - problem at the annotation step

Question

[rajini28m]

Hi Everyone,

I am doing structural variant detection using different programs such as DELLY, Softsearch, Svseq. After detection I am integrating the SV calls from all programs using the R package Intansv. It is working fine up to the last step, but is giving me error while annotating. Please see error below. I am consistently getting same error so many times.

If some one has used this program and have figure out how to do it. Please post your answer.

Thanks

Raj

dellysinc_chk_merge <- methodsMerge(rtx430dellytest, rtx430_svseq_chr1, rtx430_softsearch, others = rtx430_sinc_tochk_withdelly, overLapPerDel = 0.8, numMethodsSupDel = 2)

svannotest_gff3 <- import.gff3 (con = "/Users/grad/Sorghum_project/Sbicolor_v2.1_ref_genome/Sbicolor_annotations/v2.1/annotation/Sbicolor_255_v2.1.gene.gff3")
head(svannotest_gff3)

> fourmethodsannot2.1 <- svAnnotation (structuralVariation = dellysinc_chk_merge$del, genomeAnnotation = svannotest_gff3)
Error in `$<-.data.frame`(`*tmp*`, "parent", value = NA) :
  replacement has 1 row, data has 0
In addition: Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

> 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] VariantAnnotation_1.14.11 Rsamtools_1.20.4          Biostrings_2.36.3         XVector_0.8.0             intansv_1.9.0             ggbio_1.16.1              ggplot2_1.0.1
 [8] plyr_1.8.3                rtracklayer_1.28.8        GenomicRanges_1.20.5      GenomeInfoDb_1.4.2        IRanges_2.2.7             S4Vectors_0.6.3           BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] reshape2_1.4.1          splines_3.2.1           lattice_0.20-33         colorspace_1.2-6        GenomicFeatures_1.20.2  survival_2.38-3         XML_3.98-1.3            RBGL_1.44.0
 [9] foreign_0.8-65          DBI_0.3.1               BiocParallel_1.2.20     RColorBrewer_1.1-2      lambda.r_1.1.7          stringr_1.0.0           zlibbioc_1.14.0         munsell_0.4.2
[17] gtable_0.1.2            futile.logger_1.4.1     OrganismDbi_1.10.0      latticeExtra_0.6-26     Biobase_2.28.0          GGally_0.5.0            biomaRt_2.24.0          AnnotationDbi_1.30.1
[25] proto_0.3-10            Rcpp_0.12.0             acepack_1.3-3.3         scales_0.2.5            BSgenome_1.36.3         Hmisc_3.16-0            graph_1.46.0            gridExtra_2.0.0
[33] digest_0.6.8            stringi_0.5-5           biovizBase_1.16.0       grid_3.2.1              tools_3.2.1             bitops_1.0-6            magrittr_1.5            RCurl_1.95-4.7
[41] RSQLite_1.0.0           dichromat_2.0-0         Formula_1.2-1           cluster_2.0.3           futile.options_1.0.0    MASS_7.3-43             reshape_0.8.5           rpart_4.1-10
[49] GenomicAlignments_1.4.1 nnet_7.3-10