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../eagle \
--bfile=EUR_test \
--geneticMapFile=USE_BIM \
--chrom=21 \
--outPrefix=phased \
--numThreads=4 \
2>&1 | tee example.log
### run eagle without any parameters to list options
### typical options for phasing without a reference:
# to import genetic map coordinates: --geneticMapFile=tables/genetic_map_hg##.txt.gz
# to remove indivs or exclude SNPs: --remove, --exclude
# to perform QC on missingness: --maxMissingPerIndiv, --maxMissingPerSnp
# to select a region to phase: --bpStart, --bpEnd
### old:
# to use Eagle1 algorithm: --v1
# to use Eagle1 fast mode: --v1fast
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