ROSMAP WGS data

ROSMAP WGS data #

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) whole-genome sequence data

Contact #

Hao Sun and Xuanhe Chen

Data Descriptions #

This data is part of WGS done for three AMP-AD supported studies: The ROSMAP study (the data provided here), the MayoRNAseq study, and the MSBB study. Provided are VCF files, consisting of all samples from that study divided by chromosome, for the following analysis. Information about overlaps of ROSMAP samples and other database can be find here Information of the preprocessing: https://github.com/cumc/fungen-xqtl-analysis/blob/main/analysis/Wang_Columbia/ROSMAP/genotype/genotype_preprocessing.ipynb

  • Data Location on CU cluster: The original VCF files of joint-call ROS/MAP WGS is here (N = 1162/4669 of them are ROS/MAP; GRCh38): /mnt/vast/hpc/bvardarajan_lab/data/Family_WGS/vcfs/vcf_b38_with_rosmap_2022/joint_vcf The intermediate VCF files for QCing the vcf can be found here: /mnt/mfs/ctcn/team/lu/project_h3k9ac/QC/output After processing through our pipeline, the processed plink file is here (N = 1160, MAC = 0, HWE = 1E-8, sample/variants missingness filter = 0.1 ; GRCh38) /mnt/vast/hpc/csg/FunGen_xQTL/ROSMAP/Genotype/ROSMAP_NIA_WGS.leftnorm.bcftools_qc.plink_qc.bed The LD matrixes calculated based on old version of this genotype (/mnt/vast/hpc/csg/FunGen_xQTL/ROSMAP/genotype/ROSMAP_NIA_WGS.leftnorm.filtered.filtered.bed) are here: /mnt/vast/hpc/csg/molecular_phenotype_calling/LD/output/1300_hg38_EUR_LD_blocks_LD
  • Data Location on MSSM cluster: The ROSMAP monocyte WGS data was downloaded in VCF format, with one file per chromosome (plus X, Y, MT). (Path on MSSM to be added)