Showing docs for version 3.6-0 | The latest version is 4.1.4.0


SplitNCigarReads

Splits reads that contain Ns in their CIGAR string

Category Sequence Data Processing Tools

Traversal ReadWalker

PartitionBy READ


Overview

This tool identifies all N cigar elements in sequence reads, and creates k+1 new reads (where k is the number of N cigar elements) that correspond to the segments of the original read beside/between the splicing events represented by the Ns in the original CIGAR. The first read includes the bases that are to the left of the first N element, while the part of the read that is to the right of the N (including the Ns) is hard clipped, and so on for the rest of the new reads.

Input

One or more bam files.

Output

A single processed bam file.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T SplitNCigarReads \
   -R reference.fasta \
   -I input.bam \
   -o output.bam \
   -U ALLOW_N_CIGARS

 

Note

When this tool is used as part of the RNAseq best practices, the command should include mapping quality reassignment. See the Best Practices documentation for details.


Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by SplitNCigarReads.

Downsampling settings

This tool does not apply any downsampling by default.


Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

SplitNCigarReads 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
Optional Flags
--doNotFixOverhangs
false do not have the walker hard-clip overhanging sections of the reads
Advanced Parameters
--maxBasesInOverhang
 -maxOverhang
40 max number of bases allowed in the overhang
--maxMismatchesInOverhang
 -maxMismatches
1 max number of mismatches allowed in the overhang
--maxReadsInMemory
 -maxInMemory
150000 max reads allowed to be kept in memory at a time by the BAM writer

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.


--doNotFixOverhangs / -doNotFixOverhangs

do not have the walker hard-clip overhanging sections of the reads

boolean  false


--maxBasesInOverhang / -maxOverhang

max number of bases allowed in the overhang
If there are more than this many bases in the overhang, we won't try to hard-clip them out

int  40  [ [ -∞  ∞ ] ]


--maxMismatchesInOverhang / -maxMismatches

max number of mismatches allowed in the overhang
If there are more than this many mismatches within the overhang regions, the whole overhang will get hard-clipped out. It is still possible in some cases that the overhang could get clipped if the number of mismatches do not exceed this value, e.g. if most of the overhang mismatches.

int  1  [ [ -∞  ∞ ] ]


--maxReadsInMemory / -maxInMemory

max reads allowed to be kept in memory at a time by the BAM writer
For expert users only! To minimize memory consumption you can lower this number, but then the tool may skip overhang fixing in regions with too much coverage. Just make sure to give Java enough memory! 4Gb should be enough with the default value.

int  150000  [ [ -∞  ∞ ] ]


--out / -o

Write output to this BAM filename instead of STDOUT

GATKSAMFileWriter  stdout


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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.