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GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf
(step 2) Genotype/haplotype calling using thunder [ thunder_glf_freq].
thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o
(1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [ MaCH website] and [ MaCH wiki].
(2) Check out example files and command lines under examples/thunder/ in the thunder package [ thunder_glf_freq].
== Important Filters ==