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GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf
GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf
minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.
(step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V009.source.tgz thunder_glf_freq].
(step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V009.source.tgz thunder_glf_freq].
