Recommendation For Cnv Calling Program Based On Depth Of Coverage From Bam
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).
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for whole genome, you may try CNVnator
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is your data Exome or WGS?
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. ?