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

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=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


#user custom class missing
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


#-samglfclean not documented
Theta is third value.


#soap usage is not documented
N0=theta/2/u/s


from psmc time to realtime


#-sites does not work without all chromsomes being in the *sites file
2*g*N0*times
#-sites gives wrong chromomosome in error


from psmc time to realtime


#phat does not work alone (-doMaf 8)
N0*lambda


# make haploid 1dsfs
=Wiki doc=
# fix wiki doc with -sites should contain -rf with curs from -sites
#  check userdir is writable
#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
# 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 28: 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 00:13, 26 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.