Questions about the raw output file(s)'s columns
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Hello, I searched for a while for a description of the columns in the "*_cnvs.tsv" output file. These are the columns:
#chr start end CN_change loglikelihood no_of_regions length_KB potential_AF genes qvalue
Some have obvious meaning, some don't (to me), is there an explanatory document somewhere?
Is CN_change code for something, or is it the actual number of copies?
loglikelihood of what?
no_of_regions, is this number of exons, or number of intervals in the input bedfile?
length_KB, length of what?
potential_AF, this seems lower than 1 always, allele frequency?
genes, I suppose this is empty unless the bed file was annotated?
qvalue, qvalue of what?
Thank you for your patience, sorry if I missed something obvious
PS. I only ask about this output file as I thought it was the best one to look through. Did I get this wrong, as well? Which of the three files makes most sense to look through?
https://github.com/imgag/ClinCNV/blob/master/doc/germline_CNV_analysis.md - here it is =) at the bottom
Perfect, thank you German, have a lovely weekend!