Description

This module is used to clip primer sequences from your alignments.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information [ id:'sample1']

bam:file

Sorted BAM file

*.bam

bai:file

BAI index of the input BAM file

*.bam.bai

bedpe:file

BEDPE file of primer pair locations

*.bed

Output

name:type
description
pattern

bam

meta:map

Groovy Map containing sample information [ id:'sample1']

*.primerclipped.bam:file

Sorted BAM file containing clipped query sequences according to the given primer pair locations

*.primerclipped.bam

bai

meta:map

Groovy Map containing sample information [ id:'sample1']

*.primerclipped.bam.bai:file

BAI index of the output BAM file

*.primerclipped.bam.bai

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bamclipper
MIT

BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing