The SplitVariants task used to have some lines to switch columns 5 and 6 of the bed file output, which is read in downstream tasks of TrainRDGenotyping.GenotypePESR. This causes the TrainRDGenotyping.GenotypePESR to error out reporting.
Error: WARNING: Incorrect CNV type specified
1: stop("WARNING: Incorrect CNV type specified")
The python script splitvariants.py was modified to switch the columns to the appropriate order to be compatible with downstream analysis requirements. The script passed testing with both womtool and cromshell on the 1kg reference panel with the bca flag set to both True and False.
The SplitVariants task used to have some lines to switch columns 5 and 6 of the bed file output, which is read in downstream tasks of TrainRDGenotyping.GenotypePESR. This causes the TrainRDGenotyping.GenotypePESR to error out reporting.
Error: WARNING: Incorrect CNV type specified 1: stop("WARNING: Incorrect CNV type specified") The python script splitvariants.py was modified to switch the columns to the appropriate order to be compatible with downstream analysis requirements. The script passed testing with both womtool and cromshell on the 1kg reference panel with the bca flag set to both True and False.