Difference between revisions of "Pcangsd"

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(Created page with "Category:SoftwareCategory:BiologyCategory:GenomicsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|pcangsd}} |{{#vardefine:url|https://github.co...")
 
 
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The estimated individual allele frequencies can further be used to account for population structure in other probabilistic methods. PCAngsd can perform the following analyses:
 
The estimated individual allele frequencies can further be used to account for population structure in other probabilistic methods. PCAngsd can perform the following analyses:
 
 
     Covariance matrix
 
     Covariance matrix
 
     Admixture estimation
 
     Admixture estimation
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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 +
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 18:21, 8 December 2023

Description

pcangsd website  

Framework for analyzing low-depth next-generation sequencing (NGS) data in heterogeneous/structured populations using principal component analysis (PCA). Population structure is inferred by estimating individual allele frequencies in an iterative approach using a truncated SVD model. The covariance matrix is estimated using the estimated individual allele frequencies as prior information for the unobserved genotypes in low-depth NGS data.

The estimated individual allele frequencies can further be used to account for population structure in other probabilistic methods. PCAngsd can perform the following analyses:

   Covariance matrix
   Admixture estimation
   Inbreeding coefficients (both per-individual and per-site)
   HWE test
   Genome-wide selection scans
   Genotype calling
   Estimate NJ tree of samples


Environment Modules

Run module spider pcangsd to find out what environment modules are available for this application.

System Variables

  • HPC_PCANGSD_DIR - installation directory
  • HPC_PCANGSD_BIN - executable directory