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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.

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'snv_results.RData' file not being generated

poojachandra opened this issue · comments

commented

Hi,
I am able to generate all the outputs except the 'snv_results.RData' file at the 'svclone cluster' step.
The pipeline does not throw any errors and 'ccube' is installed as well.

Is there anything else I might be missing ?

Thank You

commented

Can you try (within your sample output directory):

find . -iname "*.RData"

The snv_results.RData file should be under the sample/ccube_out/snvs subdirectory. If it isn't there, is the RData file for SVs present? Is the snvs RData file being generated for the example data run with run_example_wsnvs.sh?