Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else reads which multimap to the contamination genome will be spuriously kept.