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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{|<!--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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===Serial=== | ===Serial=== | ||
| + | * gcc/5.2.0 | ||
* {{#var:app}} | * {{#var:app}} | ||
| + | <!-- | ||
===Parallel (OpenMP)=== | ===Parallel (OpenMP)=== | ||
* intel | * intel | ||
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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'''] | |
|}} | |}} | ||
Revision as of 15:40, 17 November 2021
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.
Required Modules
Serial
- gcc/5.2.0
- AdmixTools
Citation
If you publish research that uses AdmixTools you have to cite it as follows:
N. Patterson et al. Genetics, vol 192:1065–1093