Changes

You should now be ready to run the first analysis step, which is to estimate phased haplotypes for each sample. The script below, named ''prototype_phasing_job.sh''(based on the [https://mathgen.stats.ox.ac.uk/impute/prephasing_and_imputation_with_impute2.tgz example script] on the IMPUTE2 website), illustrates how to do this. It requires three parameters (chromosome number, interval start and interval end) and assumes that input data files will in a directory called <code>data_files</code>, with results in <code>results</code> directory and estimated haplotypes in a <code>sampled_haps</code> directory. It has been modified to specify the build 37 recombination map should be used and to include the <source>-allow_large_regions</source> parameter.

You should now be ready to run the first analysis step, which is to estimate phased haplotypes for each sample. The script below, named ''prototype_phasing_job.sh''(based on the [https://mathgen.stats.ox.ac.uk/impute/prephasing_and_imputation_with_impute2.tgz example script] on the IMPUTE2 website), illustrates how to do this. It requires three parameters (chromosome number, interval start and interval end) and assumes that input data files will in a directory called <code>data_files</code>, with results in <code>results</code> directory and estimated haplotypes in a <code>sampled_haps</code> directory. It has been modified to specify the build 37 recombination map should be used and to include the <source>-allow_large_regions</source> parameter.

<source lang="bash">

<source lang="sh">

#!/bin/bash

#!/bin/bash

#$ -cwd

#$ -cwd