Eric Talevich
Eric Talevich
The usual ways to reduce noise are: * Refine the reference profile -- ideally use 10-30 good-quality normal samples, a reference genome FASTA, and an exclusion list of known problematic...
Samples are normalized by total sequencing coverage, so if sample1 had higher coverage overall, the log2 copy *ratio* in that area of chr5 could still be similar, in this case...
Are there any blank fields in your .cnr file? Which columns do they occur in?
I would guess FigTree is not attempting to parse the support values into floating-point numbers, just keeping and displaying the values as strings. It would be possible to represent multiple...
Related: #436
I merged a possible fix in #914. Could you try pulling the latest development version and see if the problem is fixed now?
Is the weight column always entirely null, or sometimes a mix of numeric values and the occasional null?
I merged a possible fix in etal/cnvkit#914 . Are you able to try the latest development version of CNVkit and see if the problem is fixed now, or does the...
Generally it's safe to say that if the .call.cns file shows a copy number of 3 or more for the chromosome, or the log2 ratio in the .cns is around...
The file .call.cns is based on the first .cns, with some additional processing: * Absolute copy number is inferred, and certain segments are marked as having neutral copy number. These...