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ReadAdaptorTrimmer

Utility tool to blindly strip base adaptors.

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ


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)]

It is assumed that when data is paired, one read will span the forward strand and one read will span the reverse strand. Hence, when specifying adaptors they should be specified as both forward and reverse-complement to make sure they're removed in all cases. By design, as well, "circular" constructions where a read can have an insert, then adaptor, then more genomic insert, are not supported. When an adaptor is detected, all bases downstream from it (i.e. in the 3' direction) will be removed. Adaptor detection is carried out by looking for overlaps between forward and reverse reads in a pair. If a sufficiently high overlap is found, the insert size is computed and if insert size < read lengths adaptor bases are removed from reads. Advantages over ReadClipper: - No previous knowledge of adaptors or library structure is necessary Advantages over 3rd party tools like SeqPrep: - Can do BAM streaming instead of having to convert to fastq - No need to merge reads - merging reads can have some advantages, but complicates downstream processing and loses information that can be used, e.g. in variant calling

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 \
   -T ReadAdaptorTrimmer \
   -I my_reads.bam \
   -R resources/Homo_sapiens_assembly18.fasta \
   -o trimmed_Reads.bam
 

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by ReadAdaptorTrimmer.

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).

ReadAdaptorTrimmer specific arguments

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
Advanced Parameters
--minMatches
15 Minimum number of substring matches to detect pair overlaps
Advanced Flags
--removeUnpairedReads
false Remove unpaired reads instead of erroring out

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


--removeUnpairedReads / -removeUnpairedReads

Remove unpaired reads instead of erroring out
If true, this argument will make the walker discard unpaired reads instead of erroring out.

boolean  false


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA