Tagged with #ugcallvariants
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Created 2012-07-23 23:57:02 | Updated 2012-07-23 23:57:02 | Tags: ugcallvariants gatkdocs
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A new tool has been released!

Check out the documentation at UGCallVariants.

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Created 2015-07-01 12:08:39 | Updated | Tags: ugcallvariants indels cnv
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I notice that although UnifiedGenotyper and HaplotypeCaller identify indels, none or reported greater than a length of around 50bp. Obviously integrating this ability into the already complicated algorithms is not easy, nor are such variants especially common - but they can easily be biologically-important, as well as interfered SNP calls, e.g. if a SNP is in a heterozygous deletion.

Do you know of any callers for larger indels/CNVs, specifically for multi-sample NGS projects ? I've looked at pindel and break-dancer (and probably a few others) but they seem mostly for single samples.