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Gatk Haplotype Caller , --downsample_to_coverage

Hello,

Just a couple quick questions regarding the --downsample_to_coverage command line argument in Gatk HaplotypeCaller.

  • what is the default value that applies if it is not specified on the command line?
    i've seen statements that say that the default is 250, but I have also seen that there is a hardcoded limit of 1000?

  • if a value different than the default is entered on the command line, does it take effect?
    I've statements in the forum stating that there is an internal limit to 1000 and that the number entered on the command line
    may not take effect?

Thanks for the clarification
Severine

Answers

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