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, 16:19, 3 October 2012
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| === Reference based chunking === | | === Reference based chunking === |
| | | |
− | In case you didn't split your data with ChunkChromosome we highly recommend to run imputation using our reference based chunking method. | + | In case you didn't split your data with ChunkChromosome, we highly recommend to run imputation using our reference based chunking method (minimac.10.3.12 or newer required) |
| + | |
| + | <source lang="bash"> |
| + | #!/bin/sh |
| + | |
| + | chromend=57000000 # for chr 20 |
| + | chunksize=7000000 |
| + | overlap=250000 |
| + | vcfref="yourvcfref.vcf" |
| + | gwas="yourgwasfilename" |
| + | out="youroutputfilename" |
| + | |
| + | for start in `seq 0 $chunksize $chromend` |
| + | do |
| + | end=$(($start+7000000)) |
| + | start=$((start+1)) |
| + | |
| + | minimac --vcfReference \ |
| + | --refHaps $vcfref \ |
| + | --snps ${gwas}.snps --haps ${gwas}.haps.gz \ |
| + | --vcfstart $start --vcfend $end \ |
| + | --vcfwindow $overlap \ |
| + | --prefix $out.$start.$end > $out.$start.$end.log & |
| + | |
| + | done |
| + | |
| + | </source> |
| | | |
| == X Chromosome Imputation == | | == X Chromosome Imputation == |