Saturday, April 26, 2014

Big-Y BAM STR Analysis Tool


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. 
Supported BAM files:
  • Big-Y BAM
  • Any BAM file with UCSC convention (hg1x) ordering for human reference genome.
Please let me know if any of the other BAM files are supported and/or the above is not supported.

Prerequisites: 
Usage:

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'.

Download:  Big-Y BAM STR Analysis (64 bit).zip (97.3 MB)

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.
References:
  • 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.
Change Log :1.0
  • Initial Release.