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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=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
#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
Line 23: Line 22:
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>


Revision as of 10:29, 12 March 2014

Wiki doc

  1. write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
  2. user custom class missing

Code fix/cleanup

  1. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor
  2. don't quit program if a chr is not included in the -sites file
  3. check all getoptions stderr output.
  4. -samglfclean not documented
  5. soap usage is not documented
  6. 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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