This tool is replaced by BAM Analysis Kit with more advanced features.
Similar to Big-Y BAM SNP Analysis Tool where you were able to analyse SNPs, this tool is for STRs.
The tool provides the following output,
- y_str.csv - contains all identified STRs in BigY BAM file.
- Big-Y BAM
- Any BAM file with UCSC convention (hg1x) ordering for human reference genome.
- Windows 64 bit Operating System
- Microsoft .Net Framework 4.0
- 10 GB of free hard disk space.
- Minimum 2 GB RAM.
Extract the download and click 'Big-Y BAM STR Analysis UI.exe'. Select the .BAM file and click 'Start Analysis'.
After clicking 'Start Analysis', a command prompt will automatically open and start executing series of commands.
After nearly an hour (depending on your computer speed), the output will be available inside a subfolder called 'out'.
Source Code: (Inside src folder)
License: The download bundles the following software for easy usage. So, if you are using this tool for non-commercial and/or personal use, you should be alight.
- Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
- Gymrek M, Golan D, Rosset S, & Erlich Y. lobSTR: A short tandem repeat profiler for personal genomes. Genome Research. 2012 April 22.
- Initial Release.