Improve Research Reproducibility A Bio-protocol resource
- Home
- Protocols
-
Request a Protocol
Ask a
question
Favorite
We estimated the heterozygosity levels in the genomes of 13 ancient individuals with coverages above 4.5× (Fig. 4A and table S1) as well as in the genomes of Loschbour (6.2×, European Mesolithic) and Stuttgart (9.2×, European Neolithic) (37). Heterozygosity levels were computed using ANGSD (49) on the alignment files (BAM) of the individuals as “angsd -i ${bamfile} -GL 1 -doGlf 2 -doMajorMinor 1 -sites $sites -doSaf 1 -anc $ref. -minQ 30 -minmapq 30 -noTrans 1 -out ${filebase}” and “realSFS ${filebase}.saf.idx -bootstrap 100 -P 16 > ${filebase}_est_boot.ml.”
Copyright and License information: ©2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).
This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
Do you have any questions about this protocol?
Post your question to gather feedback from the community. We will also invite the authors of this article to respond.
Post a Question0 Q&A
