I am trying to use the bam-window for the first time to prepare the input files for the copyCat package for CNV calling. I do not see much of a documentation resource for running the bam-window. I tried to run on my tumor bam file and was thrown with an error. I would like to know if anyone has information for a manual or a link where I can go through the errors usually faced and how to proceed with it. I could not make much out from google and hence the question. In any case if anyone is willing to answer here I would just put the command and the error here.
softwares/bam-window/build/bin/bam-window tumor.realigned.recal.bam ( Does it not work with GATK reclibrated and realigned bam files?)
ERROR: failed to get library name for read group tumor