ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.

User:Thorfinn: Difference between revisions

From angsd
Jump to navigation Jump to search
No edit summary
 
(69 intermediate revisions by 2 users not shown)
Line 1: Line 1:
#phat does not work alone (-doMaf 8)
=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


# make haploid 1dsfs
N0=theta/regionsize/4/u
# fix wiki doc with -sites should contain -rf with curs from -sites
 
#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
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=
# 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  
# from morten shitoutput  
<pre>
h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
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 = 8 10 5  has less than 3 blocks. skipping
Line 16: Line 58:
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1…
h1…
</pre>


# fix -doFasta for single chromosomes. put gzwrite && bufstr.l =0 whenever we change chr
=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.