Changes

Some of command line options are explained below and others are self-explanatory.

Some of command line options are explained below and others are self-explanatory.

   

   

  -c : minimum cutoff of posterior probability to output a variant [Default: 0.5]

  -c : minimum cutoff of posterior probability to output a variant [''Default: 0.5'']

  --theta : scaled mutation rate per site [Default: 0.001]

  --theta : scaled mutation rate per site [''Default: 0.001'']

  --tstv: prior of ts:tv ratio [Default: 2.0]

  --tstv: prior of ts:tv ratio [''Default: 2.0'']

  --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

  --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. [Default: 1e-08]

  --rate_denovo : mutation rate per haplotype per generation. [''Default: 1e-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]

  --min_denovo_LLR : 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 ==