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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,

Best Answer


  • Hi Geraldine,

    thank you for your reply.
    I am doing three rounds of BQSR because I don't have any database of variants for my species. This solution is suggested in my case in the GATK documentation fro BQSR. I hope I understood well this advise ! I did three rounds since I could see a convergence or a plateau, meaning that the number of calls made by UG after the 3rd round is nearly equal to the number of calls got after the 2nd round.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah okay, that makes sense. Just checking :)

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