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 | |||
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= | =Wiki doc= | ||
# check userdir is writable | |||
# write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files | # write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files | ||
#user custom class missing | #user custom class missing | ||
=Code fix/cleanup= | =Code fix/cleanup= | ||
#if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ? | |||
#if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor | |||
# don't quit program if a chr is not included in the -sites file | # don't quit program if a chr is not included in the -sites file | ||
#check all getoptions stderr output. | #check all getoptions stderr output. | ||
# from morten shitoutput | # from morten shitoutput | ||
<pre> | <pre> | ||
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
- 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
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
- make haploid 1dsfs
- simplefy filereading. from glf files
- fix -doFasta for single chromosomes.