Question: True variant not called by Varscan
gravatar for braveen.joseph
13 months ago by
braveen.joseph20 wrote:


I'm using the Varscan tool to call SNPs and INDELs. There are some TRUE variants that are not called by this variant caller. I can clearly see them with IGV. For example there are 34 reads at a loci with all being mutant reads (100%), and still not called as a variant. I used a minimum read depth of 3 and a base quality score of 24 to call these variants. The reads seems to be in good quality. This variant is still not called even if I reduce the base quality score. Can some one explain me the reason, why this variant might not have been called.


varscan galaxy • 395 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by braveen.joseph20
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Varscan uses other filters besides just the ones you mention. You could try tuning those to see what results are produced. Reviewing the pileup content may also provide some information. That tool also has parameters that can be tuned.

Running the data through a different variant caller (or a few others) might also be informative. Tutorials that cover variant analysis can be reviewed here: with linked resources.

For example, to capture all variation and filter after (mostly, there are some options for filtering with these tools, too), try Naive Variant Caller followed by Variant Annotator.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
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