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PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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calling gridss_annotate_vcf_repeatmasker #593

Closed MjelleLab closed 2 years ago

MjelleLab commented 2 years ago

Hi, how do I call gridss_annotate_vcf_repeatmasker? I am trying this:

gridss_annotate_vcf_repeatmasker -j gridss-2.13.2-gridss-jar-with-dependencies.jar -o annotated.vcf Sample-112_GRIDSS.all_calls.vcf

But get:

-bash: /home/local/.../.../gridss_annotate_vcf_repeatmasker: Permission denied