ImputationPipeline – bbmri

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Version 38 (modified by a.kanterakis, 13 years ago) (diff)
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This page describes the Imputation pipelines developed by the GoNL - Impute team. Please contribute. For help with trac wiki formatting: http://trac.edgewall.org/wiki/WikiFormatting
All scripts presented here are located in our SVN repository: http://www.bbmriwiki.nl/svn/imputation
Minutes of our Team Calls: http://www.bbmriwiki.nl/wiki/Imputations/Minutes

Location: http://www.bbmriwiki.nl/svn/Imputation/alex/scripts/Normalize_beagle_datasets.ftl
Takes a list of beagle and marker files and applies the following checks:
Checks if the SNPs are compatible. If the compatibility cannot be corrected by SNP inversion then it is discarded.
Checks if SNP has null alleles, if so, SNP is removed from study data.
Checks if two SNPs with same reference code (rs) are in the same position.
Checks if two SNPs in the same position have the same reference code (rs).
Checks if a SNP in the study has MAF < MAF_minimum, HWE < HWE_minimum and CR < CR_minimum if any of these criteria are met, the SNP is discarded. (MAF = Minor Allele Frequency, HWE = Hardy Weinberg Equilibrium, CR = Call Rate)

It generates a log file with all inconsistencies found: At the end of this file there is a summary of the problems found:

SNPs inverted: For Example A/G SNPs in reference , T/C SNPs in study
Allele problems: Number of SNPs with inconsistent alleles in study and in reference that could not be fixed with flipping
Position problems (different references, same loci): As it says. These SNPs are NOT removed. We keep the reference (rs number) of the reference panel
Unresolved single alleles problems: SNPs in study that have only one allele. These SNPs are filtered out.
Double rs codes problems: As it says. This SNPs are filtered out.
SNPs in study with MAF < MAF_minimum: SNPs with MAF < MAF_minimum set.
SNPs in study with HWE < HWE_minimum: SNPs with HWE < HWE_minimum set.
SNPs in study with CR < CR_minimum: SNPs with Call Rate < CR_minimum set
SNPs that differ in Allele Frequencies: SNPs with difference in AF between reference and study over CR_minimum set.

Options:

input_beagle_study : The study in beagle format
input_beagle_reference : The reference in beagle format
input_markers_study : The study's markers in beagle format
input_markers_reference : The reference's markers in beagle format
output_beagle_study : The Normalized output of the study (Use this as "study" for imputation)
output_beagle_reference : The Normalized output of the reference (Normally you will not use this file)
output_markers_study : The Markers of the normalized study
output_markers_reference : The Markers of the normalized reference
output_log_filename : the log filename