User:Jonathan R. I. Coleman/Notebook/Notes and Protocols/2014/06/27
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Converting from IMPUTE2 .impute2 format to single-value genotype formatJoni Coleman, King's College London (Please send comments to jonathan[dot]coleman[at]kcl[dot]ac[dot]uk)
Comments look like this Commands (on the UNIX command line) look like this
[0 * p(AA)] + [1 * p(AB)] + [2 * p(BB)] which simplifies to: p(AB) + [2 * p(BB)]
zcat impute2.gen.gz | awk '{printf $1"\t"$2; for(i=6; i<NF; i+=3) {printf "\t"$(i+0)*0+$(i+1)*1+$(i+2)*2}; printf "\n"}' | bgzip > dosages.gz 1. Unzips the impute2 file 2. Prints the chromosome number (NB. "---" for unaltered imputed genotypes in impute2 file) and the SNP name (in Phase3 release, this is also the BP positions and alleles) 3. Iterates through the impute2 file and makes single-value dosage score for each line. 4. Gzips the output file.
zcat impute2.gen.gz | awk '{printf $1"\t"$2"\t"$3"\t"$4"\t"$5; for(i=6; i<NF; i+=3) {printf "\t"$(i+0)*0+$(i+1)*1+$(i+2)*2}; printf "\n"}' | bgzip > dosages.gz 1. Implementation is as above, but the SNP name in earlier releases only contains rs ID, so this adds the BP and alleles to the file.
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