CallableLoci on Triticum species

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Barbara Iadarola

• March 17, 2021 11:48

Dear All,

I am analysing a Triticum Aestivum sample (NGS data from targeted resequencing). I tried to use the CallableLoci from GATK v3.8 to calculate callability of all chromosomes. The tool outputs only "NO_COVERAGE" and "REF_N" after going beyond position 535Mb for all chromosomes, even if I have reads covering some regions. So it seems like there is some error in the coverage calculation of regions beyond 535Mb.

This never happened for other NGS human samples analysed, so I don't understand where the problem could be. I tried to give 20Gb of RAM to the software, but I don't know if this could be the problem, because the output file is complete, but wrong.

Could you please help me with this issue?

Thank you very much,

Barbara

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• 

  Genevieve Brandt (she/her)

  • March 17, 2021 20:33

  Hi Barbara,

  We do not provide active support for GATK3 anymore. I would recommend updating to GATK 4.2, which is our current version. If you need to use GATK3, you can search for answers from our archived legacy forum: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/

  Best,

  Genevieve

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