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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Difference between HC and UG methods

When I compared the result of HaplotypeCaller and Unifiedgenotyper, I found some locus that only be calling variation by UG. However, the origin bam file and bamout file produced by reassembly both contain this variation(see the figure 1). The number of reads supporting reference and alter allele are 456(87%) and 69(13%) respectively in raw bam. Meanwhile they are 439(86%) and 69(14%) in bamout file. I have got confused with this problem.


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