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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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manta and canvas #5

Closed ghost closed 8 years ago

ghost commented 8 years ago

Hi

I am wondering the main difference between Manta and Canvas. I've got the literatures for both and actually Manta user for a large dataset. My understanding is Canvas takes a bin-based approach (RD method?) .. Also, the supplementary document of Canvas has few benchmark tables but no comparison with Manta. Just wondering how the performance is different between two tools.

Thanks

StephenTanner commented 8 years ago

Manta is a structural variant (SV) caller that uses breakpoints (partially aligned reads, or cases where read 1 aligns and read 2 aligns elsewhere). Canvas is a copy number variant (CNV) caller based mainly on coverage (and also on b allele frequency - e.g. at copy number 3, allele frequencies cluster around 33% and 66% instead of 50%). In practice, the two tools work well together - Manta for copy number changes up to ~10kb and other SVs like translocations, Canvas for larger (>10kb) copy number variants.

ghost commented 8 years ago

Thanks Steve