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

From angsd
Jump to navigation Jump to search
No edit summary
No edit summary
Line 15: Line 15:




# make haploid 1dsfs
 
# fix wiki doc with -sites should contain -rf with curs from -sites
# fix wiki doc with -sites should contain -rf with curs from -sites
#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?  
#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?  
Line 46: Line 46:


# better screen output if unsorted filtering
# better screen output if unsorted filtering
=addtional method=
# make haploid 1dsfs

Revision as of 16:15, 5 March 2014

Wiki doc

  1. write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
  2. -sites does not work without all chromsomes being in the *sites file
  3. user custom class missing

Code fix

  1. -samglfclean not documented
  1. soap usage is not documented


  1. -sites does not work without all chromsomes being in the *sites file
  2. -sites gives wrong chromomosome in error



  1. fix wiki doc with -sites should contain -rf with curs from -sites
  2. describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
  3. 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…

  1. fix -doFasta for single chromosomes. put gzwrite && bufstr.l =0 whenever we change cur
  1. -doMaf 4 is not working if post is not external
  1. Regarding an open issue of printing %e instead o numbers, using the bombyx/lyca dataset:
  1. fix }else{
   fprintf(stderr,"./a.out [make_bed|do_stat|validate_bed|print]\n");
 }  in thetaStat
  1. simplefy filereading. from glf files
  1. check 1offseted in -sites file
  2. add more info to -sites file output
  1. better screen output if unsorted filtering

addtional method

  1. make haploid 1dsfs