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Thank you, so what would be the steps? I ran IGV and the read looks properly mapped. But what I shall do after? Even if I make the VCF, wha…
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recount has TCGA raw data: https://bioconductor.org/packages/devel/workflows/vignettes/recountWorkflow/inst/doc/recount-workflow.html
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You are probably hitting this issue https://github.com/snakemake/snakemake/issues/1899. Perhaps you are using an old version of snakemake w…
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Make sure you have proper indentation, when I run your code and fix the indentation it works fine.
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