If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
Unified Genotyper with Galaxy: callable base and depth of coverage after BQSR
I am using GATK through the Galaxy main server to analyze variations from whole-genome re-sequencing of various samples of non-model species (nematodes worms).
I would like to know whether it is possible to have with Galaxy's GATK tools a kind of pileup (base per base or intervall, like .bed) of genome indicating specifically which base where callable or not by Unified Genotyper (UG), such as "CallableLoci".
The log & metrics files generated by UG in Galaxy give the general statistics of callable loci, but there is no such a file giving a detailed information of the eligibility of each base.
In the same kind of idea, I would like to get a per-locus-depth of coverage (which can partially help answering my previous question, although it does not take into account all the filters used by UG such as base quality, mapping quality, etc.). This tool is available on Galaxy. However, I am performing 3 rounds of BQSR to get my final vcf file. Shall I calculate the depth of coverage using the first BAM file before BQSR or the last recalibrated BAM file obtained in the 3rd round of BQSR? I don't think BQSR alter the coverage score, so I would say this shouldn't matter. Am I right?
Thanks in advance for help and advices,