copywriteR - gsudre/autodenovo GitHub Wiki
09/13/2017
This one was quite easy to run. Need to do a more in-depth check of the results, and also need to check if setting up all samples as control and samples is the best way to do this. Their wiki seems to say it's fine, but it's worth testing.
library("CopywriteR")
bp.param <- SnowParam(workers = 12, type = "SOCK")
samples = '/data/NCR_SBRB/fake_trios/project2/final/CCGO_800818/CCGO_800818-ready.bam'
controls = samples
sample.control <- data.frame(samples, controls)
preCopywriteR('/data/NCR_SBRB/fake_trios/copywriter', 5000, 'hg38', prefix = "chr")
CopywriteR(sample.control, '/data/NCR_SBRB/fake_trios/copywriter/', '/data/NCR_SBRB/fake_trios/copywriter/hg38_5kb_chr/', bp.param)
For reference, here's the vignette: https://bioconductor.org/packages/release/bioc/manuals/CopywriteR/man/CopywriteR.pdf