CNV detection for amplicon sequence datas without bed file
Hello,
I want to detect CNV from normal and tumor amplicon-based samples. I tried to use two of the tools (cnvkit, covcopcan) but it didn't give a good result because I don't have a target bed file. I would be appreciated if you recommend me any tools to find CNV without using a bed file or ways to create a target bed file.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
What are the steps for Germline and Somatic CNV detection using CNVkit?
written by ahmad mousavi
-
CNVkit analysis with different average depths of control normals
written by luna •
-
CNVkit methods and parameters
written by ICfc97 •
-
CNVkit detected CNV number
written by enes •
-
CNVKit for unmatched tumor-only WGS samples
written by vctrm67 •
-
how should I filter call.cns results according to cn depth p_ttest probes weight
written by linouhao •
-
CNVkit with tumor only bam and flat reference
written by youki •
-
confused about how to run pipeline
written by andrew.lamb •
-
CNVkit GRCh38 tumor-normal pair
written by plink_9857
-
Jointly Detect Somatic Copy Number Variations
written by lyz10302012
well.. isn't it the real problem ?
Unfortunately it is :(. That is why i asked here to find a solution.
You can re-create a bed file yourself. It is quite commonly done. Identify regions well covered in both samples, divide them into parts, I don't remember exactly how long amplicons usually are but maybe around 80bp.
For amplicons it can be done actually quite accurately due to the PCR-based nature of the amplification - start/end of the amplicon should have straight peaks of reads starting exactly there.
Thank you for your answer. I will try this with using bedtools genomecov.