Hi,
I'm trying to read a VCF file that was produced by GATK (HaplotypeCaller on several samples then GenotypeGVCFs to merge them, and then VariantFiltration and SelectVariants to filter and select single samples), with readVcf.
I'm getting this error:
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, :
key 42 (char '*') not in lookup table
Here's my sessionInfo:
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] stringr_1.0.0 data.table_1.9.6 VariantAnnotation_1.10.5
[4] Rsamtools_1.16.1 Biostrings_2.32.1 XVector_0.4.0
[7] GenomicRanges_1.16.4 GenomeInfoDb_1.0.2 IRanges_1.22.10
[10] BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.26.1 magrittr_1.5 zlibbioc_1.10.0
[4] GenomicAlignments_1.0.6 BiocParallel_0.6.1 BSgenome_1.32.0
[7] brew_1.0-6 foreach_1.4.3 sendmailR_1.2-1
[10] tools_3.2.0 fail_1.3 checkmate_1.7.1
[13] Biobase_2.24.0 DBI_0.3.1 iterators_1.0.8
[16] BatchJobs_1.6 digest_0.6.9 rtracklayer_1.24.2
[19] base64enc_0.1-3 bitops_1.0-6 codetools_0.2-14
[22] RCurl_1.95-4.7 biomaRt_2.20.0 RSQLite_1.0.0
[25] stringi_1.0-1 BBmisc_1.9 GenomicFeatures_1.16.3
[28] stats4_3.2.0 XML_3.98-1.3 chron_2.3-47
Help would be appreciated.
