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We should explore whether it might be better to use:
The --pick option to give one effect per variant;
The --fields option to output the data as a csv.
A script to perform allele specific anal…
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Remove this from JSON output:
`myKrobe.predictor for Staphylococcus, version 0.0.0.1`
`Command: /home/phelimb/Mykrobe-predictor_clonal_model/bin/Mykrobe.predictor.staph --list /data2/users/zam/staph_a…
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--file
Command: /home/phelimb/myKrobe-predictor/bin/Mykrobe.predictor.staph --file /Net/wombat/dipro/mmm/gorm/v3/dat/Saur/stampy/00003000/C00003100_R00000022.bam --install_dir /home/phelimb/myKrobe-pr…
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./Mykrobe.predictor.tb --file /Net/wombat/dipro/mmm/gorm/v3/dat/Mtub/stampy/00023000/C00023875_R00000039.bam --install_dir ~/dev/git/myKrobe-predictor --method InSilicoOligos
myKrobe.predictor for …