Hello,

I try to run CINdex software for chromosomal instability analysis ( https://www.bioconductor.org/packages/release/bioc/html/CINdex.html , https://rdrr.io/bioc/CINdex/src/R/run.cin.chr.R) Currently, I am stuck with preparation of input data. According to CINdex manual in Github, the input should be the "result of any segmentation algorithm such as CBS,FMR. Should be a data frame of 3 column-lists or matrix of three-column lists" I have whole exome VCF and BAM files from subject group (sequencing performed on peripheral blood DNA for germline variants), but do not have control group sequenced.

I started looking at all kinds of R packages, but the minus is that they are mostly supposed for tumors, and you need both cancer and normal samples as input. I only have WES VCF and BAM from patient group. Some packages even looked suitable. I tried PureCN, but failed to install and is quite difficult for a beginner. VariantAnnotation did not like my VCFs for some reason, it showed that 0 ranges are found for samples.

Therefore, I am still in search of appropriate software or R package, where it is possible to obtain GRange object as 3 column-list (or matrix of three-column lists) from WES VCF or BAM files.

Any help will be appreciated.