
Michael Apostolides
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Latest activity by Michael Apostolides
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Michael Apostolides commented,
The run command is missing the -i flag: java -jar cromwell.jar run simpleVariantSelection.wdl simpleVariantSelection_inputs.json ..should be... java -jar cromwell.jar run simpleVariantSelection.wdl...
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Michael Apostolides commented,
As an added note, the gatk command should look like this, with the corresponding GATK4 syntax changes: java -jar ${GATK} HaplotypeCaller \ -R ${RefFasta} \ -I ${inputBAM} \ ...
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Michael Apostolides commented,
GATK has been updated to GATK4. It should be noted that "GenomeAnalysisTK.jar" file no longer exists in this version.
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