varscan copynumber producing highly variable data
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7.2 years ago

I ran varscan copynumber on my high coverage, whole genome paired end data (matched normal @ 30x & tumor @ 65x after duplicate removal) using default parameters and followed the workflow on the varscan webpage (copynumber, copycaller, DNAcopy segmentation following the R code sample from Chris).  Plotting the output using DNAcopy plot function revealed that the seg means are extremely noisy and over-segmented (looks like a cloud ranging from -2 to 2 on a log2 scale).  Oddly enough, the chrUn chromosomes produce much more 'normal' looking plots with a red seg mean line (instead of a cloud) that is mostly around 0.  I suspect that maybe the default parameters are not appropriate for high coverage genome-wide data?  I'm not sure what to change though.  Should I modify '--max-segment-size' and/or '--min-segment-size' in varscan copycaller?  Any ideas?

varscan copynumber • 2.6k views
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7.2 years ago
poisonAlien ★ 3.1k

Hi,

Did you normalize your data for differences in library size ( as you mentioned normal 30X and tumor 65X) ?

VarScan2 copynumber has a parameter --data-ratio which accounts for this difference.

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Yes, sorry I should have included that in my post.  I used --data-ratio to adjust for the difference in sequence coverage.  All other options were default.

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