bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

Abstract

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: bammds-users@nongnu.org Supplementary information: Supplementary data are available at Bioinformatics online.