search

weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
187 stars 72 forks source link

Chromosome coding UKBB #443

Open nandobonf opened 7 months ago

nandobonf commented 7 months ago

Hi all, In the analysis of UKBB data, when specifying the chromosome (--chrom, step2), the script requires a leading "0" for one-digit chromosomes (1-9), otherwise it throws an error. It took me a while to debug this. Please fix or add details in the help.

singularity run -B $(pwd):/in saige.1.3.0.sif Rscript /usr/local/bin/step2_SPAtests.R \
--bgenFile=ukb_c1_b0_v3.bgen \
--bgenFileIndex=ukb_c1_b0_v3.bgen.bgi \
--sampleFile=ukb_c1_b0_v3_s487203.sample \
--AlleleOrder=ref-first \
--SAIGEOutputFile=out_assoc_c1.txt \
--chrom=01 \
--GMMATmodelFile=/in/output/step1.rda \
--varianceRatioFile=/in/output/step1.varianceRatio.txt \
--is_Firth_beta=TRUE \
--pCutoffforFirth=0.01 \
--is_output_moreDetails=TRUE \
--LOCO=TRUE