Changes between Version 36 and Version 37 of ImputationPipeline

Dec 6, 2011 12:01:51 PM (12 years ago)



  • ImputationPipeline

    v36 v37  
    88== Reference data ==
    99== Pre processing ==
     10=== Normalize beagle datasets ===
     11 * Location: [[BR]]
     12 Takes a list of beagle and marker files and applies the following checks:
     13 * Checks if the SNPs are compatible. If the compatibility cannot be corrected by SNP inversion then it is discarded.
     14 * Checks if SNP has null alleles, if so, SNP is removed from study data.
     15 * Checks if two SNPs with same reference code (rs) are in the same position.
     16 * Checks if two SNPs in the same position have the same reference code (rs).
     17 * 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)
     19It generates a log file with all inconsistencies found: At the end of this file there is a summary of the problems found:
     20 * '''SNPs inverted''': For Example A/G SNPs in reference , T/C SNPs in study
     21 * '''Allele problems''': Number of SNPs with inconsistent alleles in study and in reference that could not be fixed with flipping
     22 * '''Position problems (different references, same loci)''': As it says. These SNPs are NOT removed. We keep the reference (rs number) of the reference panel
     23 * '''Unresolved single alleles problems''': SNPs in study that have only one allele. These SNPs are filtered out.
     24 * '''Double rs codes problems''': As it says. This SNPs are filtered out.
     25 * '''SNPs in study with MAF < MAF_minimum''': SNPs with MAF < MAF_minimum set.
     26 * '''SNPs in study with HWE < HWE_minimum''': SNPs with HWE < HWE_minimum set.
     27 * '''SNPs in study with CR < CR_minimum''': SNPs with Call Rate < CR_minimum set
     28 * '''SNPs that differ in Allele Frequencies''': SNPs with difference in AF between reference and study over CR_minimum set.
    1129== Imputation software ==
    1230 * Impute2