Difference between revisions of "AdmixTools"
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(Created page with "Category:SoftwareCategory:BioinformaticsCategory:GenomicsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|AdmixTools}} |{{#vardefine:url|http://...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|AdmixTools}} | |{{#vardefine:app|AdmixTools}} | ||
| − | |{{#vardefine:url| | + | |{{#vardefine:url|https://github.com/DReichLab/AdmixTools}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
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|{{#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--> | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | The package contains 6 programs: | |
| + | *convertf: See README.CONVERTF for documentation of programs for converting file formats. | ||
| + | *qp3Pop: See README.3PopTest for details of running f_3 test. This test can be used as a format test of admixture with 3 populations. | ||
| + | *qpBound: See README.3PopTest for details of running qpBound. This test can be used for estimating bounds on the admixture proportions, given 3 populations (2 reference and one target). | ||
| + | *qpDstat: See README.Dstatistics for details of running D-statistics. This is a formal test of admixture with 4 populations. | ||
| + | *qpF4Ratio: See README.F4RatioTest for details of running F4 ratio estimation. This program computes the admixture proportion by taking the ratio of two f4 tests. | ||
| + | *rolloff: See README.ROLLOFF/ README.ROLLOFF_OUTPUT for details for running rolloff. This program can be used for dating admixture events. | ||
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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://genetics.med.harvard.edu/reich/Reich_Lab/Software_files/2012_Patterson_AncientAdmixture_Genetics.pdf N. Patterson et al. ''Genetics'', vol 192:'''1065–1093'''] | |
|}} | |}} | ||
Latest revision as of 20:50, 11 August 2022
Description
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Environment Modules
Run module spider AdmixTools to find out what environment modules are available for this application.
System Variables
- HPC_ADMIXTOOLS_DIR - installation directory
Citation
If you publish research that uses AdmixTools you have to cite it as follows:
N. Patterson et al. Genetics, vol 192:1065–1093