ANGSD: Analysis of next generation Sequencing Data

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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=
# angsd: angsd_realSFS.cpp:980: void realSFS::algoGeno(int, double**, char*, char*, int, int, kstring_t*, int, int*, int*, double*): Assertion `pest!=__null' failed. this means, ask for -pest if -doSaf 3
#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.
#-samglfclean not documented
#soap usage is not documented
# from morten shitoutput  
# from morten shitoutput  
<pre>
<pre>
Line 23: 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 alignement of output
<pre>
-> [analysisKeepList.cpp] -sites is still beta, use at own risk...
Filter file contains major/minor information to use these in analysis supper '-doMajorMinor 3'
-> Reading fasta: /space/genomes/refgenomes/hg19/gatk/hg19.fa
Will call genotypes using sample allele frequencies
-> Parsing 33 number of samples
-> Printing at chr: 1 pos:566303 chunknumber 1800Segmentation fault (core dumped)
</pre>
Problem with command:
<pre>
./angsd0.585/angsd -sites filt2 -b list -doMajorMinor 4 -doMaf 2 -GL 1 -r 22: -out res9/res22 -doGeno 19 -doPost 1 -doGlf 1 -doSaf 3 -P 6 -pest res1.1/all.saf.em.ml -doCounts 1 -dumpCounts 4 -ref  /space/genomes/refgenomes/hg19/gatk/hg19.fa
</pre>
<pre>
-nan | 0.333333 0.333333 0.333333 |1.098612 | 0 |
[emFrequencyNoFixed] caught nan will exit
w0 0.000000 w1 0.000000 w2 0.000000
</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

  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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