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This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information.
This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information.
=== (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://csg.sph.umich.edu//yli/GPT_Freq.011.source.tgz GPT_Freq] ===
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
