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Update script to make SNP caller commands: add command line options to pass to caller & mpileup.

Thomas Sebastian Schmidt requested to merge tschmidt/metaSNV:master into master

This commit allows to pass command line options through the bash script metaSNP_SNP directly to the caller and to mpileup. The following options are introduced:

  • minimum coverage (“-c”, default 4)
  • minimum threhold (“-t”, default 4)
  • minimum frequency (“-p”, default 0.01)
  • maximum depth per position and sample for mpileup (“-d”, mirroring mpileup -d option, default 20,000)
  • rename debugging option from “-d” to “-D”

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