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Jump to navigationJump to searchPolymutt: a tool for calling polymorphism and de novo mutations in families for sequencing data (view source)
Revision as of 18:26, 18 June 2011
, 18:26, 18 June 2011→Other options
-c : minimum cutoff of posterior probability to output a variant
-c : minimum cutoff of posterior probability to output a variant
--theta : scaled mutation rate per site
--theta : scaled mutation rate per site
--tstv: prior of ts:tv ratio. Default is 2.0
--nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files.
--nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files.
--de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON
--de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON
--rate_denovo : mutation rate per haplotype per generation. Usually it is on the order of 1e-08
--rate_denovo : mutation rate per haplotype per generation. Usually it is on the order of 1e-08
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. Default is 2.0
--min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output
--min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output
