truncdeme

Intro

Section about "invade-td.jar"

parameters

:::bash
--- Mandatory ---
--genome              the size of the chromosomes, e.g 'MB:2,3,1,5'; also
                      feasible kb or bp; mandatory
--N                   the population size; mandatory
--gen                 how many generations to run the simulations; mandatory
--basepop             the starting insertions, eg 'seg:40'; mandatory

--- Optional ---
--demes               the number of demes ; default=1
--sampleid            the sample id ; default=na
--u                   the transposition rate; default=0.0
--v                   the excision rate; default=0.0
--fl-id               prefered mobilization of either FL or ID; 0.5 no bias,
                      0.4 prefered mobilization of ID; default=0.5
--conversions         the conversion rate; rate at which FL transpositions
                      are converted to full length; default=0.0
--min-full-length     the amount of full length insertions required per individual;
                      if smaller TE is not active; default=1
--min-fraction-fl     the minimum fraction of full length insertions; default=null
--mfwd                migration rate - forward; migrants = N*m; default=0.0
--mrev                migration rate - backwards; migrants = N*m; default=0.0
--rep                 how often should the simulations be repeated; default=1
--rr                  recombination rate for each chromosome, e.g 'cM:3,4,4,5'
                      ; default=none
--cluster             piRNA cluster regions; default=none
--xf                  deleterious effect of a full length insertion; default=0.0
--xd                  deleterious effect of internally deleted insertion;
                      default=0.0
--steps               sample output every xx generation; default=20
--migsteps            perform a migration event every xx generation; default=1
--replicate-offset    the replicate count is shifted by the given number;
                      allows pseudo-parallelization; replicate starts at
                      offset + 1; default=0
--seed                random seed; default=System.currentTimeMillis()
--min-w               the minimum average fitness of a population; ; default=0.3
--trunc-file          output file with the position and abundance of the
                      internal deletions; default=none
--mig-trunc-file      output file with the position and abundance of the
                      internal deletions of migrants; default=none
--mhp-file            Manhatten plot file; show position and popfreq of TE
                      insertions; default=none
--mhp-count           number diploid indivdiuals to sample for the Manhatten
                      plot; default=N
--silent              only report the final output
--help                print the help

Standard output

1   0   |1  0.267   0.025   0.267   1.00    0.3 0.0 0.0 |2  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |3  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |4  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |5  0.000   0.000   0.000   1.00    0.0 0.0 0.0 
1   20  |1  0.915   0.208   0.657   1.00    2.6 0.2 1.5 |2  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |3  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |4  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |5  0.000   0.000   0.000   1.00    0.0 0.0 0.0 
1   40  |1  0.999   0.577   0.752   1.00    9.1 0.8 7.7 |2  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |3  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |4  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |5  0.000   0.000   0.000   1.00    0.0 0.0 0.0 
1   60  |1  1.000   0.799   0.723   1.00    15.8    1.5 14.5    |2  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |3  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |4  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |5  0.000   0.000   0.000   1.00    0.0 0.0 0.0 
1   80  |1  1.000   0.893   0.744   1.00    21.6    2.1 20.2    |2  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |3  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |4  0.000   0.000   0.000   1.00    0.0 0.0 0.0 |5  0.000   0.000   0.000   1.00    0.0 0.0 0.0 
1

• col1: replicate
• col2: generation
• col3: sample id
• col4: placeholder, indicating that the info for deme 1 follow
• col5: fraction of individuals with TE insertion
• col6: fraction of individuals with piRNA cluster insertion
• col7: fraction of individuals with at least one full length insertion
• col8: fraction of individuals with at least one internally deleted insertion
• col9: average fitness
• col10: average insertions per diploid
• col11: average cluster insertions per diploid
• col12: average number of internally deleted copies per diploid individual
• col13: unique internal deletions in the population
• col14: fixed cluster insertions
• col15: unique insertion sites in the population
• col16: average population frequency
• col17: placeholder, indicating that the infor for deme 2 follow
• ....

Output file: --trunc-file

For example:

1       80      5       all       1       2907    0
1       100     1       all       1       2907    23277
1       100     1       id       1318    1465    159
1       100     1       id       1343    1824    1096
1       100     1       id       539     2676    4

• col1: replicate
• col2: generation
• col3: deme number
• col4; flag either all, fl or id
  • all indicates that the provided counts (col7) refer to the total number of insertions in the deme; This is useful to compute the frequency of a truncation in the population, ie: trunc-count divided by this coverage value
  • id indicates that the provided counts refer to an actual truncation
  • fl indicates that the provided counts refer to full length insertions
• col5 start position of truncation (ignore for col4 flag 0)
• col6 end position of truncation (ignore for col4 flag 0)
• col7 counts of the truncation (or with col4 flag 0, the total number of TE insertions, full-length + intneral deleted, in the deme)