Splits reads that contain Ns in their CIGAR string
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.
One or more bam files.
A single processed bam file.
java -jar GenomeAnalysisTK.jar \ -T SplitNCigarReads \ -R reference.fasta \ -I input.bam \ -o output.bam \ -U ALLOW_N_CIGARS
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.
These Read Filters are automatically applied to the data by the Engine before processing by SplitNCigarReads.
This tool does not apply any downsampling by default.
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.
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 | |
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.
do not have the walker hard-clip overhanging sections of the reads
boolean false
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 [ [ -∞ ∞ ] ]
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 [ [ -∞ ∞ ] ]
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 [ [ -∞ ∞ ] ]
Write output to this BAM filename instead of STDOUT
GATKSAMFileWriter stdout