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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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


-3) check strlen in filter -sites
N0=theta/regionsize/4/u


-2) add --help and --version
30000.0/30000000.0/4.0/u=10000


-1) check that close gzclose on a null pointer
from ms to realtime and realsize


0) set -outfiles=NULL in setargsstruct
tk are times from ms e.g. 0.01,0.06,0.2,1,2


0) fix return value
alpha are sizes from ms e.g. 0.1,1,0.5,1,2


1) write error estimation on wiki, need more info
truetimes in years


3. -filter to site
4*g*N0*tk


4. add single pars
from ms to real populationsize


alpha*N0


5.
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
<pre>
<pre>
-> angsd version: 0.567 build(Dec  7 2013 18:15:43)
h1 h2 h3 = 7 10 5 has less than 3 blocks. skipping
-> No '-out' argument given, output files will be called 'angsdput'
h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
-> Filterfile: filt supplied will generate binary representations...
h1 h2 h3 = 10 11 5 has less than 3 blocks. skipping
-> Parsing chr:'1'
h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
-> Parsing chr:'2'
h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
-> Parsing chr:'3'
h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
-> Parsing chr:'4'
h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
-> Parsing chr:'5'
h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
-> Parsing chr:'6'
h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
-> Parsing chr:'7'
h1 h2 h3 = 9 10 6 has less than 3 blocks. skipping
-> Parsing chr:'8'
h1…
-> Parsing chr:'9'
-> Parsing chr:'10'
-> Parsing chr:'11'
-> Parsing chr:'12'
-> Parsing chr:'13'
-> Parsing chr:'14'
-> Parsing chr:'15'
-> Parsing chr:'16'
-> Parsing chr:'17'
-> Parsing chr:'18'
-> Parsing chr:'19'
-> Parsing chr:'20'
-> Parsing chr:'21'
-> Parsing chr:'22'
-> Parsing chr:'X'
-> Filtering complete: Observed: 23 different chromosomes from file:filt
-> [analysisKeepList.cpp] Reading binary representation:filt
-> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
Filterfile contains major/minor information
-> [analysisKeepList.cpp] -filter is still beta, use at own risk...
Error: For sequence data (bam,SOAP) likehoods (-GL) must be specified for frequency estimation
thorfinn@pontus:~/gc_angsd$ ./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
DEV VERSION might not work thorfinn feb 1 2013 sizeof(funkypars):128
Command:
./angsd0.567/angsd -filter filt -bam list -doMajorMinor 3 -doMaf 2 -GL 1
-> angsd version: 0.567 build(Dec  7 2013 18:15:43)
-> No '-out' argument given, output files will be called 'angsdput'
-> [analysisKeepList.cpp] Reading binary representation:filt
-> [analysisKeepList.cpp] nChr: 23 loaded from binary filter file
Filterfile contains major/minor information
</pre>
</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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