Locations - orenlivne/ober GitHub Wiki

Web Tools

• Hutterite variant annotation tool: http://oberlab-dev3.uchicago.edu/annotate
  • William, Catherine and Carole have the username and password.

CRI Permanent Storage (bios.cri.uchicago.edu)

• /group/ober-resources/users/olivne - this directory contains all data and output from the programs

• /group/ober-resources/users/olivne/imputed-override - Hutterites final imputed genotype CGI data set

• /group/ober-resources/users/olivne/data-sets - useful Hutterite imputed genotype data subsets

• /group/ober-resources/users/olivne/data-sets/qc-pruned - variants that passed QC and pruned for LD

• /group/ober-resources/users/olivne/data-sets/qc - all variants that passed QC

• /group/ober-resources/users/olivne/data-sets/common-novel-qc - variants with MAF>=5%, not in CEU, passed QC

• /group/ober-resources/users/olivne/data-sets/qc-pruned-po - same as qc-pruned, but parental-origin data

• /group/ober-resources/users/olivne/old - ignore this directory (old tests)

/group/ober-resources/users/olivne/id-coefs - identity coefficient files

• Kinship files - from Gaixin
• /group/ober-resources/users/olivne/id-coefs/detailed-idcoefs-primal.txt - PRIMAL-generated detailed identity coefficients for the 1415 genotyped Hutterites

/group/ober-resources/users/olivne/out - Hutterites phasing and imputation useful intermediate results

• /group/ober-resources/users/olivne/out/phasing - phased haplotypes (at the Affymetrix SNPs)
• /group/ober-resources/users/olivne/out/requests - small data sets extracted for lab members
• /group/ober-resources/users/olivne/out/index_segments - IBD dictionary, indexed as cliques at each Affy SNP
• /group/ober-resources/users/olivne/out/impute_cgi - CGI data
• /group/ober-resources/users/olivne/out/impute_cgi/genotypes - 98 CGI sequences (NOT imputed)
• imputed-override - PRIMAL imputated data (77% call rate)
• imputed-override2 or 3 - PRIMAL+LD imputated data (85% call rate)

/group/ober-resources/users/olivne/data - Hutterites phasing and imputation input data

• /group/ober-resources/users/olivne/data/common/map - Genetic map (from HapMap)
• /group/ober-resources/users/olivne/data/hutt-affy-overlap - Affymetrix 3-chip overlap (used to phase)
• /group/ober-resources/users/olivne/data/hutt-affy-union - Affymetrix 3-chip union (used to augment imputation)
• /group/ober-resources/users/olivne/data/rsng - RS&G SNPs (used in the past for cross-validation)
• /group/ober-resources/users/olivne/data/lung - Lung cancer study - IDs