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MRCIEU / godmc

GoDMC analysis pipeline
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imputed using minimac #5

Closed ejh243 closed 8 years ago

ejh243 commented 8 years ago

In the config file what should I set for imputation quality scores and quality type? (rows 29 and 32?)

explodecomputer commented 8 years ago

hey i guess these sections?

# Imputation quality scores
# This should be a file with three columns, SNP, MAF and quality scores
quality_scores="${home_directory}/input_data/data.info"

# The software used to to estimate imputation quality
quality_type="impute2"

if you are using minimac imputed data then create a file called e.g. data.info, with three columns where the quality scores column is the rsq value. and the quality_type can be set to minimac