Help with gatk CreateSequenceDictionary
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12 weeks ago
Chris ▴ 260

Hi Biostars,

I checked my path to the hg38.fa but still don't know what cause the error. Would you please have a suggestion? Thank you so much.

gatk CreateSequenceDictionary R=/variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa O=/variant_calling/Desktop/demo/supporting_fi
les/hg38/hg38.dict

Invalid argument 'R=/variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa'

GATK • 317 views
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Entering edit mode
12 weeks ago
MatthewP ★ 1.4k

maybe try?:

-R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg38.dict
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It worked! Thanks Matt!

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