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.

Bugs: Difference between revisions

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Please don't hesitate to write if you have bugs.
Please don't hesitate to write if you have bugs.
=Bugs=
=Bugs=
==New stuff==
* Check auto generation of tai file
* Do downsampling
* make calibration matrix


* fix queing of finished threads. MAYBE_FIXED
=Limitation=
* fix numSites==0 when using regions
* check probs with gatk likelihoods in combination with realSFS
* check files are closed properly
The above will not have an effect on the results. For large number of samples, the -nQueueSize can be used. If memory is a problem.
 
==Limitation==
* RG tags are not implemented, we doubt we will ever support this.
* RG tags are not implemented, we doubt we will ever support this.
* We have observed problems for rna data. This will be fixed at some point but is not a priority.
==small changes that would be nice==
* check numSites==0 in all generals: derived classes.


* check if subdirs exists in outputfiles. Otherwise subtle crash. Done
=small changes that would be nice=
* write about single bam -i on wiki
* should rna be implemented
* make faster the filter output (ok yoda) FIXED >0.500
* make program wait for finished threads when changing chromosomes FIXED >0.500
* modify the chromo to the index instead of the chr* FIXED >0.500
* Problems opening indexfile: smallNA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam.bai

Revision as of 19:18, 5 March 2014

Contact

Please don't hesitate to write if you have bugs.

Bugs

Limitation

  • RG tags are not implemented, we doubt we will ever support this.

small changes that would be nice

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