Split Reads with N in Cigar
Category Read Data Manipulation
OverviewSplits reads that contain Ns in their cigar string (e.g. spanning splicing events in RNAseq data). Identifies all N cigar elements and creates k+1 new reads (where k is the number of N cigar elements). 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. Used for post-processing RNA reads aligned against the full reference.
BAM file with reads split at N CIGAR elements and CIGAR strings updated.
gatk SplitNCigarReads \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -O output.bam
This Read Filter is automatically applied to the data by the Engine before processing by SplitNCigarReads.
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|
|BAM/SAM/CRAM file containing reads|
|Write output to this BAM filename|
|Reference sequence file|
|Optional Tool Arguments|
||read one or more arguments files and add them to the command line|
|-1||Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.|
|40||Size of the cloud-only prefetch buffer (in MB; 0 to disable).|
|false||If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.|
||false||If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!|
||false||do not have the walker soft-clip overhanging sections of the reads|
|20||If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection|
||Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.|
|false||display the help message|
|ALL||Interval merging rule for abutting intervals|
|One or more genomic intervals over which to operate|
||40||max number of bases allowed in the overhang|
||1||max number of mismatches allowed in the overhang|
||false||have the walker split secondary alignments (will still repair MC tag without it)|
|false||refactor cigar string with NDN elements to one element|
||false||If true, don't emit genotype fields when writing vcf file output.|
|false||skip the 255 -> 60 MQ read transform|
||false||display the version number for this tool|
|Optional Common Arguments|
||true||If true, adds a PG tag to created SAM/BAM/CRAM files.|
||true||If true, adds a command line header line to created VCF files.|
|true||If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.|
|false||If true, create a MD5 digest for any BAM/SAM/CRAM file created|
|true||If true, create a VCF index when writing a coordinate-sorted VCF file.|
|false||If true, create a a MD5 digest any VCF file created.|
|Read filters to be disabled before analysis|
||false||Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)|
|One or more genomic intervals to exclude from processing|
||A configuration file to use with the GATK.|
|0||Amount of padding (in bp) to add to each interval you are excluding.|
|0||Amount of padding (in bp) to add to each interval you are including.|
|UNION||Set merging approach to use for combining interval inputs|
|false||Lenient processing of VCF files|
||0||If non-zero, partitions VCF output into shards, each containing up to the given number of records.|
||false||Whether to suppress job-summary info on System.err.|
|Read filters to be applied before analysis|
||Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.|
|SILENT||Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.|
||10.0||Output traversal statistics every time this many seconds elapse|
||Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.|
||Temp directory to use.|
|false||Whether to use the JdkDeflater (as opposed to IntelDeflater)|
|false||Whether to use the JdkInflater (as opposed to IntelInflater)|
||INFO||Control verbosity of logging.|
||150000||max reads allowed to be kept in memory at a time by the BAM writer|
||false||display hidden arguments|
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.
--add-output-sam-program-record / -add-output-sam-program-record
If true, adds a PG tag to created SAM/BAM/CRAM files.
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
read one or more arguments files and add them to the command line
--cloud-index-prefetch-buffer / -CIPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
--create-output-bam-index / -OBI
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
--disable-bam-index-caching / -DBIC
If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
--disable-read-filter / -DF
Read filters to be disabled before analysis
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
--disable-tool-default-read-filters / -disable-tool-default-read-filters
do not have the walker soft-clip overhanging sections of the reads
--exclude-intervals / -XL
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals (e.g. -XL myFile.intervals).
A configuration file to use with the GATK.
--gcs-max-retries / -gcs-retries
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
--help / -h
display the help message
--input / -I
BAM/SAM/CRAM file containing reads
R List[GATKPath] 
--interval-exclusion-padding / -ixp
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
--interval-merging-rule / -imr
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
--interval-padding / -ip
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
--interval-set-rule / -isr
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
- Take the union of all intervals
- Take the intersection of intervals (the subset that overlaps all intervals specified)
--intervals / -L
One or more genomic intervals over which to operate
--lenient / -LE
Lenient processing of VCF files
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 [ [ -∞ ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
--output / -O
Write output to this BAM filename
R GATKPath null
have the walker split secondary alignments (will still repair MC tag without it)
Whether to suppress job-summary info on System.err.
--read-filter / -RF
Read filters to be applied before analysis
--read-index / -read-index
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
--refactor-cigar-string / -fixNDN
refactor cigar string with NDN elements to one element
This flag tells GATK to refactor cigar string with NDN elements to one element. It intended primarily for use in a RNAseq pipeline since the problem might come up when using RNAseq aligner such as Tophat2 with provided transcriptomes. You should only use this if you know that your reads have that problem.
--reference / -R
Reference sequence file
R GATKPath null
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--sequence-dictionary / -sequence-dictionary
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--showHidden / -showHidden
display hidden arguments
If true, don't emit genotype fields when writing vcf file output.
--skip-mapping-quality-transform / -skip-mq-transform
skip the 255 -> 60 MQ read transform
This flag turns off the mapping quality 255 -> 60 read transformer. The transformer is on by default to ensure that uniquely mapping reads assigned STAR's default 255 MQ aren't filtered out by HaplotypeCaller.
Temp directory to use.
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
display the version number for this tool
GATK version 188.8.131.52-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.