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{:bash}

:map

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

primary_aligned_bam{:bash}

: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{:bash}

: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

primary_filtered_bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information

${prefix}.bam{:bash}

:file

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

*.{bam,cram,sam}

contamination_bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information

${prefix2}.bam{:bash}

:file

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

*.{bam,cram,sam}

versions_bamcmp{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bamcmp{:bash}

:string

The tool name

echo 2.2{:bash}

:string

The version used (constant)

versions_samtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

bamcmp{:bash}

:string

The tool name

echo 2.2{:bash}

:string

The version used (constant)

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

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
maintainer
Github user sppearce
get in touch
Ask a question on Slack Open an issue on GitHub