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Convert Illumina Beeline final report to PLINK format using beelinetools: https://github.com/pgxcentre/beelinetools
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| #!/bin/bash | |
| zcat ${1} | ./beelinetools.py convert -i - -m /resources/arrays/HumanCore-12-v1/HumanCore-12-v1-0-B.csv -o /tmp | |
| timestamp=$(date +%F-%T | tr -d ':') | |
| mv /tmp/from_stdin.ped ${2}_${timestamp}.ped | |
| mv /tmp/from_stdin.map ${2}_${timestamp}.map |
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