general_purpose_scripts

General purpose scripts

cojo-prepare.sh

Given a table with meta-analysis results for independent hits, create an extended table containing information about known signals in a specified bp window around hits.

$ cojo-prepare.sh -i <input table> -o <output table> -k <known signals> -w <bp window>

• input table: a tab separated table containing meta-analysis results for independent hits; should contain following columns:
  • column 1: panel
  • column 2: protein
  • column 5: UniProt ID of the protein
  • column 6: chromosome of the hit
  • column 8: position of the hit
  • column 10: effect allele
  • column 11: other allele
  • column 12: frequency of the effect allele
  • column 16: beta
  • column 17: standard error
  • column 18: p-value
  • column 24: number of missing samples in meta-analysis of the current hit
• output table: a tab separated table containing
  • record ID of the form: PANEL_PROTEIN_CHR_POS, where CHR and POS refer to the genomic position of the independent hit from the input table
  • CHR: chromosome of the signal (either input hit, or conditioning variant)
  • POS: position of the signal (either input hit, or conditioning variant)
  • A1: effect allele
  • A2: other allele
  • freq: allele frequency of the effect allele
  • beta: effect size
  • SE: standard error of the effect size
  • p-value
  • N: number of samples analyzed <-- redundant
  • sample names: comma-separated list of samples used in the meta-analysis
• known signals: a BED file containing information about known associations; should at least contain the following fields:
  • 1: chromosome of the known signal
  • 2: pos-1, where pos is the position of the known signal
  • 3: position of the known signal
  • 5: UniProt ID of the associated protein
• optional bp window restricting conditioning known signals (default: 1Mbp)

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cojo-wrapper.sh

Given an output table from the cojo-prepare.sh step, perform GCTA cojo-cond testing of the independent hits conditioned on known signals.

$ cojo-wrapper.sh -f <PLINK bfile prefix> -o <output directory> -i <input m/a table>

• PLINK bfile prefix: prefix filename of bed/bim/fam PLINK files
• output directory: directory with the intermediate PLINK files and result GCTA files, also contains cojo-wrapper.log and cojo-wrapper.err log files. cojo-wrapper.err contains information about failed GCTA runs
• input m/a table: output table from the cojo-prepare.sh run

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cojo-slct.sh

A simple wrapper for GCTA cojo-slct analysis, intended to be used when cojo-wrapper.sh fails because of collinearity between conditioning variants.

$ cojo-slct.sh -i <signal ID> -n <number of samples> -f <PLINK bfile prefix>

• signal ID: ID of the failed signal of the form PANEL_PROTEIN_CHR_POS (these IDs form the first column of cojo-wrapper.err error file of the previous cojo-wrapper.sh run)
• number of samples: number of samples used in the m/a analysis
• PLINK bfile prefix: prefix filename of bed/bim/fam PLINK files