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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 13:45, 13 July 2011
, 13:45, 13 July 2011no edit summary
Scaled mutation rate : --theta [1.0e-03]
Scaled mutation rate : --theta [1.0e-03]
Prior of ts/tv ratio : --tstv [2.00]
Prior of ts/tv ratio : --tstv [2.00]
de novo mutation : --denovo, --denovo_rate [0.00],
de novo mutation : --denovo, --rate_denovo [0.00],
--denovo_tstv [2.00], --denovo_min_LLR [1.00]
--tstv_denovo [2.00], --minLLR_denovo [1.00]
Optimization precision : --prec [1.0e-04]
Optimization precision : --prec [1.0e-04]
Multiple threading : --nthreads [4]
Multiple threading : --nthreads [4]
--nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files [''Default: 1']
--nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files [''Default: 1']
--de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON
--denovo : 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. [''Default: 1.5e-08'']
--rate_denovo : mutation rate per haplotype per generation. [''Default: 1.5e-08'']
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0'']
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0'']
--min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0'']
--minLLR_denovo : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0'']
== Output files ==
== Output files ==
