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cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
http://cancerit.github.io/alleleCount/
GNU Affero General Public License v3.0
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Scipt convertAlleleCounts.r deleted? #75

Closed justalilibit closed 1 year ago

justalilibit commented 1 year ago

Hi!

I have noticed that the script for convertAlleleCounts.r is not found anymore. However, the step is still listed on the nextflow website under "outputs docs". Is there a reason it was deleted? Is it still available somewhere?

davidrajones commented 1 year ago

Hi, @justalilibit .

convertAlleleCounts.r was never part of alleleCount itself. As a group we haven't written the nf-core pipeline or contributed to it I'm afraid. A quick delve into the nf-core docs shows me it seems to have existed as part of the Sarek pipeline. The link to the script fron that documentation leads us to the script page which doesn't exist anymore. I would suggest contacting the maintainers of the Sarek pipeline. I hope you find a solution.

Regards,

David