From Genome Analysis Wiki
Jump to navigationJump to search
376 bytes added
, 08:05, 5 August 2011
Line 16: |
Line 16: |
| awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps | | awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps |
| mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps | | mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps |
− | minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix imputation-results | + | minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix imputation-results |
| </source> | | </source> |
| | | |
Line 26: |
Line 26: |
| # Phase each chunk in parallel | | # Phase each chunk in parallel |
| foreach chunk (chunk*-chr1.dat) | | foreach chunk (chunk*-chr1.dat) |
− | mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r}.haps & | + | mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r}.haps >& ${chunk:r}-mach.log & |
| end | | end |
| + | wait |
| | | |
| # Impute each chunk in parallel | | # Impute each chunk in parallel |
| foreach chunk (chunk*-chr1.dat) | | foreach chunk (chunk*-chr1.dat) |
− | minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps ${chunk:r}.haps.gz --snps ${chunk:r}.snps --rounds 5 --states 200 --prefix ${chunk:r}-results | + | minimac --autoClip autoChunk-chr1.dat \ |
| + | --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --rounds 5 --states 200 \ |
| + | --haps ${chunk:r}.haps.gz --snps ${chunk}.snps --prefix ${chunk:r}-results >& ${chunk:r}-minimac.log & |
| end | | end |
| + | wait |
| + | </source> |
| + | |
| + | The ''autoChunk'', generated by the ChunkChromosome program, tells minimac what are the markers of interest for each chunk. This allows chunks to overlap (which improves accuracy near the edges) but still ensures that each marker is only imputed once. |
| | | |
| == Download == | | == Download == |