Changes

== Other options ==

== Other options ==

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 for single nucleotide variants [''Default: 0.001'']

--indel_theta : scaled mutation rate per site for Indels (works only for VCF input) [''Default: 0.0001'']

  --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']

  --denovo : 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'']

  --minLLR_denovo : 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'']

  --chr2process: the chromosome names to process. Default is empty and is to process all chromosomes in the input.

  --pos : a file with two columns (chr pos) to output genotypes of all individuals, even if the sites are monomorphic

                If multiple chromosomes are provided, they should be separated by comma, e.g. --chr2process 2,10 or --chr2process chr2,chr10

--all_sites : If turned on, all sites with at least one read coverage will be output.

 

  --gl_off : If turned on, not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations

  --gl_off: not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations

== Output files ==

== Output files ==