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=Other Tools=
=Other Tools=
Since many of our tools still rely on GLF files and samtools stopped supporting GLF files, we created a version of samtools that still supports pileup to GLF files AND incorporates the updated BAQ logic. This version is called samtools-hybrid That code can be downloaded at: https://github.com/statgen/samtools-0.1.7a-hybrid
* samtools-hybrid - Since many of our tools still rely on GLF files and samtools stopped supporting GLF files, we created a version of samtools that still supports pileup to GLF files AND incorporates the updated BAQ logic. This version is called samtools-hybrid That code can be downloaded at: https://github.com/statgen/samtools-0.1.7a-hybrid
*[[baseQualityCheck]] - tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers)
*[[baseQualityCheck]] - tool to calculate the observed base quality vs. empirical base quality (helps to evaluate mappers)
