550
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac: 1000 Genomes Imputation Cookbook (view source)
Revision as of 16:19, 3 October 2012
, 16:19, 3 October 2012→Reference based chunking
=== 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 ==
