Question: Are SV tools as thorough in CNV detection as CNVkit?
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gravatar for syntax
4 months ago by
syntax50
Boston
syntax50 wrote:

In reading through the documentation of tools like Illumina Manta, DNAnexus Parliament, Delly, Mobster - they make reference to CNV as one of the types of structural variation that can be detected.

However, when I read through CNVkit's documentation it is extremely thorough and specific to amplifications and deletions.

How do these more general SV tools compare to CNVkit? Our use case is "moving beyond SNP/LD-based GWAS" into CNV.

cnv manta parliament cnvkit sv • 191 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by syntax50

Oh, GATK4 is introducing germline and somatic CNV detection that outputs to vcf.

ADD REPLYlink written 4 months ago by syntax50
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