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12 bytes added, 16:04, 15 October 2010
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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.
=== (step 1) Site promotion using software glfMultiples [ GPT_Freq]. ===
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 [ thunder_glf_freq]. ===
thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o

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