ANGSD: Analysis of next generation Sequencing Data

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User:Thorfinn: Difference between revisions

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(Created page with "Thorfinns angsd todolist 1) write error estimation on wiki, need more info 2) Rscript ../../angsd0.565/R/estError.R Loading required package: remix Loading required package...")
 
 
(103 intermediate revisions by 2 users not shown)
Line 1: Line 1:
Thorfinns angsd todolist
=ms and psmc stuff=
./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l


1) write error estimation on wiki, need more info
N0=theta/regionsize/4/u


2)
30000.0/30000000.0/4.0/u=10000


Rscript ../../angsd0.565/R/estError.R
from ms to realtime and realsize
Loading required package: remix
 
Loading required package: plyr
tk are times from ms e.g. 0.01,0.06,0.2,1,2
Loading required package: survival
 
Loading required package: splines
alpha are sizes from ms e.g. 0.1,1,0.5,1,2
Warning message:
 
no function found corresponding to methods exports from ‘ascii’ for: ‘show’
truetimes in years
-> needed arguments:
 
file : the ancError File
4*g*N0*tk
->  optional arguments (defaults):
 
out ( errorEst ) : Name of the out files
from ms to real populationsize
indNames ( ind ) : postFix, file with names or comma seperated names of individuals
 
nIter ( 100 ) : Numer of optimazation attemps
alpha*N0
subset ( NA ) : comma seperated numbers of the individuals to include
 
main ( Error rate using an outgroup (Chimp) and a perfect man ) :
from psmc to realtime and realsize:
maxErr ( 0.02 ) : maximum allowed error rate
 
height ( 7 ) : height of the pdf
PA 4+25*2+4+6 0.026254885 0.003600825 21.895293401 5.782425186 2.106578468 0.452471596 0.479814497 0.401498376 0.367130222 0.302637758 0.336141050 0.585819704 1.405835053 2.909550136 4.044915857 4.137850214 3.776532973 3.123633638 2.466466904 2.013826351 1.792827385 1.762345431 1.839956170 1.916823191 1.921452795 1.902858530 2.051184729 2.597031978 3.508703366 4.125487051 6.375234256
width ( 11 ) : width of the pdf
 
cex ( 1 ) : scale of names
Theta is third value.
 
N0=theta/2/u/s
 
from psmc time to realtime
 
2*g*N0*times
 
from psmc time to realtime
 
N0*lambda
 
=Wiki doc=
#  check userdir is writable
# write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
#user custom class missing
 
=Code fix/cleanup=
#if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
# don't quit program if a chr is not included in the -sites file
#check all getoptions stderr output.
# from morten shitoutput
<pre>
h1 h2 h3 = 7 10 5 has less than 3 blocks. skipping
h1 h2 h3 = 8 10 5 has less than 3 blocks. skipping
h1 h2 h3 = 10 11 5 has less than 3 blocks. skipping
h1 h2 h3 = 7 12 5 has less than 3 blocks. skipping
h1 h2 h3 = 10 12 5 has less than 3 blocks. skipping
h1 h2 h3 = 10 13 5 has less than 3 blocks. skipping
h1 h2 h3 = 10 15 5 has less than 3 blocks. skipping
h1 h2 h3 = 7 10 6 has less than 3 blocks. skipping
h1 h2 h3 = 8 10 6 has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6 has less than 3 blocks. skipping
h1…
</pre>
 
=Addtional methods and functionality=
# make haploid 1dsfs
# simplefy filereading. from glf files
# fix -doFasta for single chromosomes.

Latest revision as of 23:13, 25 January 2018

ms and psmc stuff

./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l

N0=theta/regionsize/4/u

30000.0/30000000.0/4.0/u=10000

from ms to realtime and realsize

tk are times from ms e.g. 0.01,0.06,0.2,1,2

alpha are sizes from ms e.g. 0.1,1,0.5,1,2

truetimes in years

4*g*N0*tk

from ms to real populationsize

alpha*N0

from psmc to realtime and realsize:

PA 4+25*2+4+6 0.026254885 0.003600825 21.895293401 5.782425186 2.106578468 0.452471596 0.479814497 0.401498376 0.367130222 0.302637758 0.336141050 0.585819704 1.405835053 2.909550136 4.044915857 4.137850214 3.776532973 3.123633638 2.466466904 2.013826351 1.792827385 1.762345431 1.839956170 1.916823191 1.921452795 1.902858530 2.051184729 2.597031978 3.508703366 4.125487051 6.375234256

Theta is third value.

N0=theta/2/u/s

from psmc time to realtime

2*g*N0*times

from psmc time to realtime

N0*lambda

Wiki doc

  1. check userdir is writable
  2. write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
  3. user custom class missing

Code fix/cleanup

  1. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
  2. don't quit program if a chr is not included in the -sites file
  3. check all getoptions stderr output.
  4. from morten shitoutput
h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 11 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1…

Addtional methods and functionality

  1. make haploid 1dsfs
  2. simplefy filereading. from glf files
  3. fix -doFasta for single chromosomes.
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