EMMAX Pipeline

This repo includes a number of scripts used to perform a mixed model regression GWAS, with alternative model masking, as published in Ravenhall et al. 2018 https://doi.org/10.1371/journal.pgen.1007172. It is primarily meant as a personal archive of those scripts for later use.

Core Pipeline

EMMAX_Pipeline.sh

• Core pipeline for performing EMMAX mixed model regression with allele masking.
• Input:
  • CHROMOSOME - Chromosome, first command-line argument
  • SUBTYPE - Subtype, second command-line argument
  • EMMAXdir - location of emmax
  • TPED - in 12 format
  • PHENO - phenotype file: <CASE/CONTROL>, no header
  • COVARS - covariates file: <CASE/CONTROL> , no header
  • OUTDIR - output directory
  • OUTPREFIX - output prefix
  • KINF - kinship matrix
  • SCRIPTDIR - directory with supporting scripts

mergePlotEMMAX.r

• Manhattan plot based on EMMAX output
• Supporting script for EMMAX_Pipeline.sh

Associated Scripts

plotSNPIntensity.r

• Plot SNP intensity for a given SNP, useful for validating classification for key candidates.
• Input:
  • out.XY.FORMAT: Rows as SNPs, Columns as 'CHR:Chromosome, POS:Basepair, ID_0:Sample0, ..., ID_N:SampleN', calls as 'intensityX,intensityY'.
  • out.GT.FORMAT: Rows as SNPs, Columns as 'CHR:Chromosome, POS:Basepair, ID_0:Sample0, ..., ID_N:SampleN', calls as ./., 0/1, 1/1 etc.
  • PLACEHOLDER.sample: Case/Control sample file, requires 'scanID' (IDs) and 'caseorcontrol' ('CASE'/'CONTROL') columns

getLambda.r

• Scrapbook of functions for calculating genomic inflation factor (lambda).
• Requires a .ps file as input.
• Functionality is present within mergePlotEMMAX.r

ProduceTopSNPs.r

• Create a refined subset of the most significant SNPs from a combined EMMAX pipeline output.

runImpute2.sh

• Run impute2 in parallel
• Input:
  • impute2dir - location of impute2
  • refDir - reference file directory, containing genetic map, .hap and .legend files
  • refName - prefix of reference files
  • mapNamePre - Pre-chromosome component of genetic map file name
  • mapNamePost - Post-chromosome component of genetic map file name
  • toImpFile - .gen file for inputation
  • outprefix - output prefix
  • psLimit - number of sub-processes to spawn