Recommendation For Cnv Calling Program Based On Depth Of Coverage From Bam

Question

[Leszek]

I'm looking for the tool able to call deletions and duplications using depth of coverage straight from BAM file. I went through many programs, but most of them require some sort of BAM and/or genome processing (ie VarScan require samtools pileup).

[Pierre Lindenbaum]

did you read: Best Copy Number Variation tools Copy Number Variation (CNV) detection using single-end sequencing data What are the recommended tools for de novo CNV analysis? what are the 'copy number detection' tools out there for exome capture NGS data. ?

[Chris Miller]

is your data Exome or WGS?

Answer 1

[liangkaiye]

for whole genome, you may try CNVnator