Description

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).

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

Output

Name
Description
Pattern

primary_filtered_bam ()

contamination_bam ()

versions ()

Tools

bamcmp Documentation

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.

doi: 10.1158/1541-7786.MCR-16-0431License: GPL v3
Authors