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(step 1) Site promotion using software glfMultiples [https://www.sph.umich.edu/csg/yli/GPT_Freq.011.source.tgz GPT_Freq].
(step 1) Site promotion using software glfMultiples [https://www.sph.umich.edu/csg/yli/GPT_Freq.011.source.tgz GPT_Freq].
GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 --sitedepth *.glf
GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf
(step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/]
== Important Filters ==
== Important Filters ==
