CNV analysis

Question

[archanaverma433]

hi, I have 5 samples of WGS data of Schizosaccharomyces pombe. I want to do CNV analysis with the DELLY tool but these samples have different number of reads - sample1 - 1.8 million sample2 - 2.8 million sample3- 8 million sample4 - 10 millions sample5 - 3.5 million So, for CNV analysis, should I first have to normalise the data and then run the pipeline or DELLY tool can deal with this?

Thank you

[Pierre Lindenbaum]

I would say that delly can deal with this a delly's first step is to call the genotype for each bam independently. It then create a collection of interval and then re-genotype each bam independently.

[archanaverma433]

thank you for the reply