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No tranches plot

zevkronenbergzevkronenberg Member
edited February 2016 in Ask the GATK team

I've run through the VQSR pipeline.
I've written out the [R] code: "-rscriptFile output.plots.snp.R"
I run the [R] code and get the gaussian mixture model plots, but NO tranche plot?

The data to make the tranches plot is in the same directory and looks OK.

After searching the [R] script I see no text related to "TITV"....?

Version information

INFO 08:21:30,408 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56

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Answers

  • No problem, I just carefully read the tranche data.

    While I've got you on the hook:

    I've seen conflicting information about left aligning indels. Does HC automatically do this? After GVCF genotyping is it wise to run left align?

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