TY - JOUR
T1 - bammds
T2 - a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
AU - Malaspinas, Anna Sapfo
AU - Tange, Ole
AU - Moreno-Mayar, José Víctor
AU - Rasmussen, Morten
AU - DeGiorgio, Michael
AU - Wang, Yong
AU - Valdiosera, Cristina E.
AU - Politis, Gustavo
AU - Willerslev, Eske
AU - Nielsen, Rasmus
N1 - Publisher Copyright:
© The Author 2014. Published by Oxford University Press.
PY - 2014/10/15
Y1 - 2014/10/15
N2 - SUMMARY: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples-typical of ancient DNA data-particularly when only low amounts of data are available for those samples.AVAILABILITY AND IMPLEMENTATION: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools).CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.
AB - SUMMARY: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples-typical of ancient DNA data-particularly when only low amounts of data are available for those samples.AVAILABILITY AND IMPLEMENTATION: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools).CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online.
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U2 - 10.1093/bioinformatics/btu410
DO - 10.1093/bioinformatics/btu410
M3 - Article
C2 - 24974206
AN - SCOPUS:84921823843
SN - 1367-4803
VL - 30
SP - 2962
EP - 2964
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
IS - 20
ER -