I'm using PureCN. I've experimented with both the release version (1.2.3) and development version (1.5.9). Each time, regardless of the version of PureCN, I run it I get the message : "VCF does not contain somatic status and no SNP blacklist provided." . When I first saw this error, I looked at the "example_vcf.vcf" VCF file provided with PureCN (under the extdata directory in the Package directory) and saw in the INFO column "SOMATIC;VT=SNP" and tried to use that observational knowledge to try to address the message. I added "SOMATIC;VT=SNP" to the INFO fields in the VCF I am using so the values in the INFO field look this this : "SOMATIC;VT=SNP;SOMETHING;SOMETHING_ELSE" . I cannot post the VCF here and "SOMETHING" and "SOMETHING_ELSE" stand for private data. Despite adding that to the INFO fields, I still get the message "VCF does not contain somatic status and no SNP blacklist provided" so my question is : "How do I make sure PureCN gets the 'somatic status' so as to make the message not appear?"
By the way, I am actually running R (and PureCN) inside a docker container with an image I built. Is there by chance a PureCN official image for improved analysis replication?
Below is my sessionInfo() in case it might be helpful.
Thanks to anyone for any help!
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid
 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
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats4 parallel methods stats graphics grDevices utils
 datasets base
other attached packages:
 PureCN_1.5.9 VariantAnnotation_1.20.1
 Rsamtools_1.26.1 Biostrings_2.42.0
 XVector_0.14.0 SummarizedExperiment_1.4.0
 Biobase_2.34.0 GenomicRanges_1.26.1
 GenomeInfoDb_1.10.1 IRanges_2.8.1
 S4Vectors_0.12.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
 Rcpp_0.12.8 AnnotationDbi_1.36.0 GenomicAlignments_1.10.0
 zlibbioc_1.20.0 BiocParallel_1.8.1 BSgenome_1.42.0
 lattice_0.20-34 tools_3.3.1 grid_3.3.1
 data.table_1.9.8 DBI_0.5-1 digest_0.6.10
 Matrix_1.2-7.1 RColorBrewer_1.1-2 rtracklayer_1.34.1
 bitops_1.0-6 biomaRt_2.30.0 RCurl_1.95-4.8
 memoise_1.0.0 RSQLite_1.1 GenomicFeatures_1.26.0