I have encountered a problem when running a recessive analysis with files in the bgen format, I am running the following script, which takes a chromosome, start and end position as inputs:
I am finding that the script fails and succeeds with different range inputs, for example with 5:109517771-125158104 the analysis fails and with 10:60494-7405944 the analysis succeeds. The analysis fails as it cannot find any variants in the region:
[INFO] Loaded 0 male, 0 female and 393461 sex-unknonw samples from /well/PROCARDIS/ukbb_full/pheno/ukbb_9922_cad_inter.ag.rvtest.pheno
[INFO] Loaded 33206 cases, 360255 controls, and 0 missing phenotypes
[WARN] -- Enabling binary phenotype mode --
[INFO] Analysis begins with [ 393461 ] samples...
[INFO] Impute missing genotype to mean (by default)
[INFO] Analysis started
[INFO] Analyzed [ 0 ] variants
[INFO] Analysis ends at: Wed Jan 31 13:35:17 2018
[INFO] Analysis took 626 seconds
RVTESTS finished successfully
Any ideas on what might be going on here?
Thanks,
Chris Grace
Bioinformatician
PROCARDIS Group
The Wellcome Trust Centre for Human Genetics
Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
Tel: +44-(0)-1865-287679
I have encountered a problem when running a recessive analysis with files in the bgen format, I am running the following script, which takes a chromosome, start and end position as inputs:
I am finding that the script fails and succeeds with different range inputs, for example with 5:109517771-125158104 the analysis fails and with 10:60494-7405944 the analysis succeeds. The analysis fails as it cannot find any variants in the region:
Any ideas on what might be going on here?
Thanks,
Chris Grace
Bioinformatician PROCARDIS Group The Wellcome Trust Centre for Human Genetics Roosevelt Drive, Oxford, OX3 7BN, United Kingdom Tel: +44-(0)-1865-287679