CNVkit methods and parameters

Question

[ICfc97]

Hi!

I've been trying CNVkit to detect CNVs in WGS data in the sample NA12878 with coverage of 5x, so I have tried the "Whole-genome sequencing and targeted amplicon capture" varying the target size and also the algorithm which is used for segmentation".

cnvkit.py batch output_bam -n -m wgs --segment-method flasso -f GRCh37.p13 --target-avg-size 6000 --scatter --diagram -d 

As a result, I obtained, a .cns file in which the ranges are followed so the variants are one after the other and that doesn't make sense. Has anyone tried these method and know which parameters work better? Thanks in advance!

Answer 1

[wanziyi89]

It might be because you used -n instead of providing a normal sample bam file with the -normal normal.bam. -n uses a flatbed of coverage instead of coverage which is expected with your assay (e.g. your set of hybrid capture probes.).