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Rare variant test software for next generation sequencing data
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bgen -recessive analysis - issue with range list #53

Open cgrace1978 opened 6 years ago

cgrace1978 commented 6 years ago

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:

chr=$1 start=$2 end=$3 sno=$4

/well/PROCARDIS/ukbb_full/scripts/rvtest/rvtests/executable/rvtest \ --inBgen /well/ukbb-wtchg/v2/imputation/ukb_imp_chr$chr_v2.bgen \ --inBgenSample /well/PROCARDIS/ukbb_full/pheno/ukbb_9922_cad_inter.ag.v4.sample \ --pheno /well/PROCARDIS/ukbb_full/pheno/ukbb_9922_cad_inter.ag.rvtest.pheno\ --pheno-name cad_intermediate \ --out /well/PROCARDIS/ukbb_full/output/ukbb_9922rvtest$sno_$chr_$start_$end.out \ --rangeList $chr:$start-$end \ --meta score \ --covar /well/PROCARDIS/ukbb_full/pheno/ukbb_9922_cad_inter.ag.rvtest.pheno \ --covar-name pc1,pc2,pc3,pc4,pc5,genotyping.array \ --noweb

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