Closed rjcorb closed 1 year ago
There are currently duplicated column names in the output of 01-annotate_variants_*_input.R. This happens when intervar and multianno files are merged:
01-annotate_variants_*_input.R
> names(clinvar_anno_intervar_vcf_df) [1] "Ref.Gene" "Func.refGene.x" "ExonicFunc.refGene.x" "Gene.ensGene.x" "avsnp147.x" [6] "AAChange.ensGene.x" "AAChange.refGene.x" "InterVar: InterVar and Evidence" "Interpro_domain.x" "AAChange.knownGene.x" [11] "Otherinfo" "var_id" "Start" "Func.refGene.y" "Gene.refGene" [16] "GeneDetail.refGene" "ExonicFunc.refGene.y" "AAChange.refGene.y" "esp6500siv2_all" "1000g2015aug_all" [21] "avsnp147.y" "Aloft_Confidence" "integrated_confidence_value" "LINSIGHT" "GERP++_NR" [26] "GERP++_RS" "SiPhy_29way_logOdds" "Interpro_domain.y" "rmsk" "Func.ensGene" [31] "Gene.ensGene.y" "GeneDetail.ensGene" "ExonicFunc.ensGene" "AAChange.ensGene.y" "Func.knownGene" [36] "Gene.knownGene" "GeneDetail.knownGene" "ExonicFunc.knownGene" "AAChange.knownGene.y" "vcf_id" [41] "evidencePVS1" "evidenceBA1" "evidencePS" "evidencePM" "evidencePP" [46] "evidenceBS" "evidenceBP" "CHROM" "START" "ID" [51] "REF" "ALT" "QUAL" "FILTER" "INFO" [56] "FORMAT" "Sample" "Stars" "final_call"
This likely was overlooked when we modified how the two data frames are merged.
Run sessionInfo() and post the output below
sessionInfo()
> sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vroom_1.6.0 optparse_1.7.3 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.1 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0 loaded via a namespace (and not attached): [1] pillar_1.9.0 compiler_4.2.3 tools_4.2.3 bit_4.0.5 lifecycle_1.0.3 gtable_0.3.3 timechange_0.2.0 pkgconfig_2.0.3 rlang_1.1.0 cli_3.6.1 rstudioapi_0.14 parallel_4.2.3 [13] withr_2.5.0 generics_0.1.3 vctrs_0.6.2 hms_1.1.3 getopt_1.20.3 rprojroot_2.0.3 bit64_4.0.5 grid_4.2.3 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4 [25] tzdb_0.3.0 magrittr_2.0.3 scales_1.2.1 colorspace_2.1-0 utf8_1.2.3 stringi_1.7.12 munsell_0.5.0 crayon_1.5.2
Provide the command used or report the bug here
There are currently duplicated column names in the output of
01-annotate_variants_*_input.R. This happens when intervar and multianno files are merged:This likely was overlooked when we modified how the two data frames are merged.
What version are you using?
Add error message here (if applicable)
Add Session info
Run
sessionInfo()and post the output below