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

meta (map)

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

versions (file)

File containing software versions

versions.yml

bam (file)

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

*.primerclipped.bam

bai (file)

BAI index of the output BAM file

*.primerclipped.bam.bai
maintainer
Github user krannich479
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Tools

bamclipper
MIT

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

github.com/tommyau/bamclipper 10.1038/s41598-017-01703-6