Utility tool to blindly strip base adaptors.
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
The input read data in BAM format. Read data MUST be in query name ordering as produced, for example with Picard's FastqToBam
A merged BAM file with unaligned reads
java -Xmx4g -jar GenomeAnalysisTK.jar \ -T ReadAdaptorTrimmer \ -I my_reads.bam \ -R resources/Homo_sapiens_assembly18.fasta \ -o trimmed_Reads.bam
This Read Filter is automatically applied to the data by the Engine before processing by ReadAdaptorTrimmer.
This tool can be run in multi-threaded mode using this option.
This tool overrides the engine's default downsampling settings.
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 details, see the list further down below the table.
|--out||SAMFileWriter||stdout||Write output to this BAM filename instead of STDOUT|
|--minMatches||int||15||Minimum number of substring matches to detect pair overlaps|
|--removeUnpairedReads||boolean||false||Remove unpaired reads instead of erroring out|
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.
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.
Write output to this BAM filename instead of STDOUT.
Remove unpaired reads instead of erroring out. If true, this argument will make the walker discard unpaired reads instead of erroring out.
GATK version 2.7-4-g46ca8c7 built at 2013/10/10 17:33:37.