Difference between revisions of "ANGSD"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|angsd}} |{{#vardefine:url|http://popgen.dk/wiki/index.php/A...") |
|||
| (9 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|angsd}} | |{{#vardefine:app|angsd}} | ||
| 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--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 22: | Line 22: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 42: | Line 32: | ||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Additional software included in this module: | |
| − | + | *contamination | |
| + | *contamination2 | ||
| + | *emOptim2 | ||
| + | *msToGlf | ||
| + | *NGSadmix | ||
| + | *printIcounts | ||
| + | *realSFS | ||
| + | *smartCount | ||
| + | *splitgl | ||
| + | *supersim | ||
| + | *thetaStat | ||
|}} | |}} | ||
| Line 69: | Line 69: | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | [http://www.biomedcentral.com/1471-2105/15/356/abstract Korneliussen et al.] ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 2014, 15:356. doi:10.1186/s12859-014-0356-4. | |
|}} | |}} | ||
Latest revision as of 12:42, 12 August 2022
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.
Environment Modules
Run module spider angsd to find out what environment modules are available for this application.
System Variables
- HPC_ANGSD_DIR - installation directory
Additional Information
Additional software included in this module:
- 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.