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    Nikolas Pontikos
    @pontikos

    Hey Adam we can chat here about Salix.
    We can even use markdown to nicely format code:

    python $SCRIPTS/generate_hapdrop.py

    https://github.com/APLevine/Salix/blob/master/run.sh#L3

    APLevine
    @APLevine
    Okay, great.
    Nikolas Pontikos
    @pontikos
    This message was deleted
    Nikolas Pontikos
    @pontikos
    Maybe you could also include the config files which are used by Merlin:
    $MERLIN -p for_simulation.ped \
    -d for_simulation.dat \
    -m for_simulation.map \
    -f for_simulation.frq \
    --bits 0 --simulate -r ${i} \
    --save --prefix $OUT/sim_${i} \
    --swap --megabytes 1000 > $OUT/run_${i}.log
    APLevine
    @APLevine
    Those files are generated by the first stage using the pedigree file as input.