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 (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

primary_aligned_bam (file)

BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)

*.{bam,cram,sam}

contaminant_aligned_bam (file)

BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)

*.{bam,cram,sam}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

primary_filtered_bam (file)

Bam file containing the reads which align better to the primary genome.

*.{bam,cram,sam}

contamination_bam (file)

Bam file containing the reads which align better to the contaminant genome.

*.{bam,cram,sam}
maintainer
Github user sppearce
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Tools

bamcmp
GPL v3

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.

github.com/CRUKMI-ComputationalBiology/bamcmp 10.1158/1541-7786.MCR-16-0431