Utility tool to blindly strip base adaptors.

## Overview

Main application is for FASTQ/unaligned BAM pre-processing where libraries have very short inserts, and hence a substantial part of the sequencing data will have adaptor sequence present.

By design, tool will only work for Illumina-like library constructs, where the typical library architecture is: [Adaptor 1]-[Genomic Insert]-[Adaptor 2 (index/barcode)]

## Input

The input read data in BAM format. Read data MUST be in query name ordering as produced, for example with Picard's FastqToBam

## Output

A merged BAM file with unaligned reads

## Examples

 java -Xmx4g -jar GenomeAnalysisTK.jar \
-R resources/Homo_sapiens_assembly18.fasta \


### Parallelism options

This tool can be run in multi-threaded mode using this option.

### Downsampling settings

This tool does not apply any downsampling by default.

## Command-line Arguments

### Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Outputs
--out
-o
stdout Write output to this BAM filename instead of STDOUT
--minMatches
15 Minimum number of substring matches to detect pair overlaps

### Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

### --minMatches / -minMatches

Minimum number of substring matches to detect pair overlaps
Argument to control strictness of match between forward and reverse reads - by default, we require 15 matches between them to declare an overlap.

int  15  [ [ -∞  ∞ ] ]

### --out / -o

Write output to this BAM filename instead of STDOUT

SAMFileWriter  stdout