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Protocols

iAdmix specifications

Information


Unique identifier OMICS_09425
Name iAdmix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sorted BAM file for sequence data or simple genotype file (rsid genotype pairs) or PLINK files (.ped and .map), population allele frequencies for common SNPs (generated using HapMap3 genotypes or other genotype datasets)
Output data Admixture coefficients for each reference population for each individual
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Vikas Bansal

Publication for iAdmix

iAdmix citations

 (3)
call_split

Clinical application of a cancer genomic profiling assay to guide precision medicine decisions

2017
PMCID: 5580078
PMID: 28890729
DOI: 10.2217/pme-2017-0011
call_split See protocol

[…] controls, and also based on a composite of tools including determining the percentage of concordant single-nucleotide variants (snvs) with respect to previously sequenced samples, inferring sex and iadmix predictions., snvs, small insertions and deletions (indels) calling was restricted to genomic regions intended to be captured by the assay (roi). copy number variants (cnvs) were called […]

library_books

Efficient analysis of large datasets and sex bias with ADMIXTURE

2016
BMC Bioinformatics
PMCID: 4877806
PMID: 27216439
DOI: 10.1186/s12859-016-1082-x

[…] that the ancestry proportions inferred using both approaches are identical. fig. 1, the projection step we describe has been recently independently implemented by bansal et al. [] in the software iadmix, using a different optimization algorithm. we compared our admixture projection implementation to the iadmix projection implementation by running unsupervised admixture on the first 1092 […]

library_books

Whole genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness

2016
Mol Psychiatry
PMCID: 5033653
PMID: 27001614
DOI: 10.1038/mp.2016.24

[…] and diagnoses were made based on dsm-iv criteria by two independent investigators and consensus with a third if necessary., ancestry of individuals was assessed using iadmix software (v0.2) with the bundled hapmap 39 population allele frequencies. all individuals most closely resembled the ceu (utah residents with northern and western european ancestry […]


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iAdmix institution(s)
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Scripps Translational Science Institute, La Jolla, CA, USA

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