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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* check numSites==0 in all generals: derived classes. | * check numSites==0 in all generals: derived classes. | ||
* check if subdirs exists in outputfiles. Otherwise subtle crash. | * check if subdirs exists in outputfiles. Otherwise subtle crash. Done | ||
* write about single bam -i on wiki | * write about single bam -i on wiki | ||
* should rna be implemented | * should rna be implemented | ||
Revision as of 23:48, 23 November 2013
New stuff
- Do downsampling
- make plink toed output. Done
- make calibration matrix
- make snpfilters. Done (partial)
- check pest prior in -realSFS documentation. Done
Bugs
- fix queing of finished threads. MAYBE_FIXED
- 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.
- 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
- 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