Difference between revisions of "ANGSD"
Moskalenko (talk | contribs) |
|||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 43: | Line 43: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | *angsd | |
| + | *contamination | ||
| + | *contamination2 | ||
| + | *emOptim2 | ||
| + | *msToGlf | ||
| + | *NGSadmix | ||
| + | *printIcounts | ||
| + | *realSFS | ||
| + | *smartCount | ||
| + | *splitgl | ||
| + | *supersim | ||
| + | *thetaStat | ||
|}} | |}} | ||
Revision as of 15:00, 18 September 2015
Description
ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes. This program is not for manipulating '.bam' files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying bamfiles.
Required Modules
Serial
- angsd
System Variables
- HPC_{{#uppercase:angsd}}_DIR - installation directory
Additional Information
- angsd
- contamination
- contamination2
- emOptim2
- msToGlf
- NGSadmix
- printIcounts
- realSFS
- smartCount
- splitgl
- supersim
- thetaStat
Citation
If you publish research that uses angsd you have to cite it as follows:
Korneliussen et al. ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 2014, 15:356. doi:10.1186/s12859-014-0356-4.