Open oghzzang opened 3 years ago
Yes, please use CN or RDCN. The long answer is:
For copy-number variants delly is currently not using the GT field because that's commonly used for hom. ALT (1/1), het. (0/1) and hom. REF (0/0). For copy-number variants I do not know the allelic distribution. For instance if the total copy-number of a segment is 8 the allelic copy-numbers could be 4 and 4, or 8 and 0, or 1 and 7, ...
Because of that issue delly only outputs the total copy-number in FORMAT:CN and the copy-number likelihoods for each copy-number state (FORMAT:CNL).
Dear @tobiasrausch,
Hi I'm Oh.
Thanks for your reply.
Have a nice day!
Oh.
Hey, I executed the same commands. However, it says, that all my samples data has low coverage, therefore I need to increase the scanning window.
I do with with "-w 50000", then it works. However all the variants are "N".
Do these Ns represent long bases or it represents "N" base ?
If it's the second one, how do i exclude this reference "N" bases?
And when i do
delly classify -f germline -o filtered.bcf c1.bcf
The result is empty. What did i do wrong?
Thankyou
I am sorry, I still need to fix the N
reference nucleotides. That's on the ToDo list. Just rely on POS and INFO/END for the size of the CNV and FORMAT/CN shows the estimated copy-number. The classify
subcommand requires a multi-sample BCF file.
Thankyou for your response. I still have some questions. As I want to find the germline CNVs for each one sample. Is this possible ? Why do we need multiple samples? I haven't found any tools that do this. Some of the tools need multiple-sample, such as DELLY.
On Wed, Oct 26, 2022 at 8:37 PM Tobias Rausch @.***> wrote:
Reopened #223 https://github.com/dellytools/delly/issues/223.
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Dear @tobiasrausch,
Hi. I'm Oh.
I executed the delly for Germline CNV calling.
I want to ask about the genotype of my called CNVs (c1.cnv.bcf), or merge the calls (merged.bcf).
All genotype of CNVs is "./." as below.
As I know, "./." is non-call.
Anyway, I only have to use "RDCN", so does it matter?
Many thanks.
Oh.