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bam-matcher website  

A simple tool for determining whether two BAM files contain reads sequenced from the same sample or patient by counting genotype matches at common SNPs.

BAM-matcher is most useful at comparing whole-genome-sequencing (WGS), whole-exome-sequencing (WES) and RNA-sequencing (RNA-seq) human data, but can also be customised to compare panel data or non-human data.

Environment Modules

Run module spider bam-matcher to find out what environment modules are available for this application.

System Variables

  • HPC_BAM-MATCHER_DIR - installation directory
  • HPC_BAM-MATCHER_BIN - executable directory
  • HPC_BAM-MATCHER_EXE - example directory
  • HPC_BAM-MATCHER_CONF - config directory


If you publish research that uses bam-matcher you have to cite it as follows:

Paul P.S. Wang; Wendy T. Parker; Susan Branford; Andreas W. Schreiber Bioinformatics 2016 doi: 10.1093/bioinformatics/btw239