Help with gatk CreateSequenceDictionary

Question

[Chris]

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'

Answer 1

[MatthewP]

maybe try?:

-R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg38.dict

[Chris]

It worked! Thanks Matt!