I want to perform finemapping for splicing-based transcriptome association study, firstly, I created the weight database using mashr-based splicing prediction model from S-predixcan using the following code:
focus import
/data2/projects/bioinfo/yyan/database/MetaXcan/models/sqtl/mashr/mashr_${tissue}.db
predixcan --name GTEx --assay rnaseq
--tissue ${tissue} --out /data2/projects/bioinfo/yyan/projects/LC_AS_WAS/focus/weight_database/GTEx_mashr_sqtl_${tissue}
the mashr_${tissue}.db was downloaded from https://predictdb.org/post/2021/07/21/gtex-v8-models-on-eqtl-and-sqtl/
then, I perform finemapping using the following code and encountered the error message:
focus finemap GCST004748_buildGRCh37_munge_clean_sumstats.gz.sumstats.gz
/data2/projects/bioinfo/xingjie/src/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.${chr} /data2/projects/bioinfo/yyan/projects/LC_AS_WAS/focus/weight_database/GTEx_mashr_sqtl_Lung.db
--trait LC --chr ${chr} --locations 37:EUR --out GCST004748_buildGRCh37_chr${chr}
I want to perform finemapping for splicing-based transcriptome association study, firstly, I created the weight database using mashr-based splicing prediction model from S-predixcan using the following code:
focus import
/data2/projects/bioinfo/yyan/database/MetaXcan/models/sqtl/mashr/mashr_${tissue}.db
predixcan --name GTEx --assay rnaseq
--tissue ${tissue} --out /data2/projects/bioinfo/yyan/projects/LC_AS_WAS/focus/weight_database/GTEx_mashr_sqtl_${tissue}
the mashr_${tissue}.db was downloaded from https://predictdb.org/post/2021/07/21/gtex-v8-models-on-eqtl-and-sqtl/
then, I perform finemapping using the following code and encountered the error message:
focus finemap GCST004748_buildGRCh37_munge_clean_sumstats.gz.sumstats.gz
/data2/projects/bioinfo/xingjie/src/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.${chr} /data2/projects/bioinfo/yyan/projects/LC_AS_WAS/focus/weight_database/GTEx_mashr_sqtl_Lung.db
--trait LC --chr ${chr} --locations 37:EUR --out GCST004748_buildGRCh37_chr${chr}