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Samtools: Local Realignment Around Indel

In samtools mpileup, adjust the option -m and -F to control when want to initiate indel realignment, any guideline to set the values for m and F for

  1. high coverage data (eg. >=20X)
  2. low coverage data (eg. <20X)

documentation at http://samtools.sourceforge.net/mpileup.shtml stated For 500 exomes, using -m 3 -F 0.0002 (3 supporting reads at minimum 0.02% frequency) is necessary to find singletons.

any hints how are this thresholds been set?


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