rcollins13 / wgd Goto Github PK

Thanks for releasing such a good repository. I am trying to develop a structural variation calling and annotation pipeline following your paper (An open resource of structural variation for medical and population genetics) using WDL and our PBS cluster, however, I stuck in some details in the SV calling part, specifically for CNV part now.

First, the 6F metadata matrices for multiCorrection.R are not available, and this Rscript needs four column instead of three. Second, cnMOPS_workflow.sh is not mentioned in the readme, are the input binCov matrix for this script from the raw output of binCov.py, or the output of the multiCorrection.R, or later output from estimatePloidy.R?

In my understanding(sorry if it is incorrect), the steps of ploidy estimation and dosage scoring model are to help us predict the gender and PCR status for sample batching information. If our data already has gender and sequencing batch information, can we skip these steps and only run cnMOPS_workflow.sh?