Clip reads in a SAM/BAM/CRAM file
Category Read Data Manipulation
Overview
Read clipping based on quality, position or sequence matching. This tool provides simple, powerful read clipping capabilities that allow you to remove low quality strings of bases, sections of reads, and reads containing user-provided sequences.There are three arguments for clipping (quality, position and sequence), which can be used alone or in combination. In addition, you can also specify a clipping representation, which determines exactly how ClipReads applies clips to the reads (soft clips, writing Q0 base quality scores, etc.). Please note that you MUST specify at least one of the three clipping arguments, and specifying a clipping representation is not sufficient. If you do not specify a clipping argument, the program will run but it will not do anything to your reads.
Quality score based clipping
Clip bases from the read in clipper from
argmax_x{ \sum{i = x + 1}^l (qTrimmingThreshold - qual)
to the end of the read. This is copied from BWA.
Walk through the read from the end (in machine cycle order) to the beginning, calculating the running sum of qTrimmingThreshold - qual. While we do this, we track the maximum value of this sum where the delta > 0. After the loop, clipPoint is either -1 (don't do anything) or the clipping index in the read (from the end).
Cycle based clipping
Clips machine cycles from the read. Accepts a string of ranges of the form start1-end1,start2-end2, etc. For each start/end pair, removes bases in machine cycles from start to end, inclusive. These are 1-based values (positions). For example, 1-5,10-12 clips the first 5 bases, and then three bases at cycles 10, 11, and 12.
Sequence matching
Clips bases that exactly match one of a number of base sequences. This employs an exact match algorithm, filtering only bases whose sequence exactly matches SEQ.
Input
Any number of SAM/BAM/CRAM files.
Output
A new SAM/BAM/CRAM file containing all of the reads from the input SAM/BAM/CRAMs with the user-specified clipping operation applied to each read.
Summary output (console)
Number of examined reads 13 Number of clipped reads 13 Percent of clipped reads 100.00 Number of examined bases 988 Number of clipped bases 126 Percent of clipped bases 12.75 Number of quality-score clipped bases 126 Number of range clipped bases 0 Number of sequence clipped bases 0
Example usage
gatk ClipReads \ -I input_reads.bam \ -O output_reads.bam \ -XF sequences.fasta \ -X CCCCC \ -CT "1-5,11-15" \ -QT 10
The command line shown above will apply all three arguments in combination. See the detailed examples below to see how the choice of clipping representation affects the output.
Detailed clipping examples
Suppose we are given this read:
314KGAAXX090507:1:19:1420:1123#0 16 chrM 3116 29 76M * * * TAGGACCCGGGCCCCCCTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA #################4?6/?2135;;;'1/=/If we are clipping reads with -QT 10 and -CR WRITE_NS, we get:
314KGAAXX090507:1:19:1420:1123#0 16 chrM 3116 29 76M * * * NNNNNNNNNNNNNNNNNTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA #################4?6/?2135;;;'1/=/Whereas with -QT 10 -CR WRITE_Q0S:
314KGAAXX090507:1:19:1420:1123#0 16 chrM 3116 29 76M * * * TAGGACCCGGGCCCCCCTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA !!!!!!!!!!!!!!!!!4?6/?2135;;;'1/=/Or -QT 10 -CR SOFTCLIP_BASES:
314KGAAXX090507:1:19:1420:1123#0 16 chrM 3133 29 17S59M * * * TAGGACCCGGGCCCCCCTCCCCAATCCTCCAACGCATATAGCGGCCGCGCCTTCCCCCGTAAATGATATCATCTCA #################4?6/?2135;;;'1/=/ClipReads 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 | |
---|---|---|---|
Required Arguments | |||
--input -I |
[] | BAM/SAM/CRAM file containing reads | |
--output -O |
null | BAM output file | |
Optional Tool Arguments | |||
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--clip-representation -CR |
WRITE_NS | How should we actually clip the bases? | |
--clip-sequence -X |
[] | Remove sequences within reads matching this sequence | |
--clip-sequences-file -XF |
null | Remove sequences within reads matching the sequences in this FASTA file | |
--cloud-index-prefetch-buffer -CIPB |
-1 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. | |
--cloud-prefetch-buffer -CPB |
40 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). | |
--cycles-to-trim -CT |
null | String indicating machine cycles to clip from the reads | |
--disable-bam-index-caching -DBIC |
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. | |
--gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
--help -h |
false | display the help message | |
--interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
--intervals -L |
[] | One or more genomic intervals over which to operate | |
--output-statistics -os |
null | File to output statistics | |
--q-trimming-threshold -QT |
-1 | If provided, the Q-score clipper will be applied | |
--read |
null | ||
--reference -R |
null | Reference sequence | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
--add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
--create-output-bam-index -OBI |
true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
--create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
--create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
--create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
--disable-read-filter -DF |
[] | Read filters to be disabled before analysis | |
--disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
--disable-tool-default-read-filters |
false | Disable all tool default read filters | |
--exclude-intervals -XL |
[] | One or more genomic intervals to exclude from processing | |
--gatk-config-file |
null | A configuration file to use with the GATK. | |
--interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
--interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
--interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
--lenient -LE |
false | Lenient processing of VCF files | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--read-filter -RF |
[] | Read filters to be applied before analysis | |
--read-index |
[] | 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. | |
--read-validation-stringency -VS |
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. | |
--seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
--sequence-dictionary |
null | Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | |
--TMP_DIR |
[] | Undocumented option | |
--use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
--use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
--verbosity |
INFO | Control verbosity of logging. | |
Advanced Arguments | |||
--showHidden |
false | display hidden arguments |
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.
--add-output-sam-program-record / -add-output-sam-program-record
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
boolean true
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--clip-representation / -CR
How should we actually clip the bases?
The different values for this argument determines how ClipReads applies clips to the reads. This can range
from writing Ns over the clipped bases to hard clipping away the bases from the BAM.
The --clip-representation argument is an enumerated type (ClippingRepresentation), which can have one of the following values:
- WRITE_NS
- Clipped bases are changed to Ns
- WRITE_Q0S
- Clipped bases are changed to have Q0 quality score
- WRITE_NS_Q0S
- Clipped bases are change to have both an N base and a Q0 quality score
- SOFTCLIP_BASES
- Change the read's cigar string to soft clip (S, see sam-spec) away the bases. Note that this can only be applied to cases where the clipped bases occur at the start or end of a read.
- HARDCLIP_BASES
- WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED. Change the read's cigar string to hard clip (H, see sam-spec) away the bases. Hard clipping, unlike soft clipping, actually removes bases from the read, reducing the resulting file's size but introducing an irrevesible (i.e., lossy) operation. Note that this can only be applied to cases where the clipped bases occur at the start or end of a read.
- REVERT_SOFTCLIPPED_BASES
- Turn all soft-clipped bases into matches
ClippingRepresentation WRITE_NS
--clip-sequence / -X
Remove sequences within reads matching this sequence
Clips bases from the reads matching the provided SEQ.
List[String] []
--clip-sequences-file / -XF
Remove sequences within reads matching the sequences in this FASTA file
Reads the sequences in the provided FASTA file, and clip any bases that exactly match any of the
sequences in the file.
String null
--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.
boolean true
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
--create-output-variant-index / -OVI
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
boolean false
--cycles-to-trim / -CT
String indicating machine cycles to clip from the reads
Clips machine cycles from the read. Accepts a string of ranges of the form start1-end1,start2-end2, etc.
For each start/end pair, removes bases in machine cycles from start to end, inclusive. These are 1-based
values (positions). For example, 1-5,10-12 clips the first 5 bases, and then three bases at cycles 10, 11,
and 12.
String null
--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.
boolean false
--disable-read-filter / -DF
Read filters to be disabled before analysis
List[String] []
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
--disable-tool-default-read-filters / -disable-tool-default-read-filters
Disable all tool default read filters
boolean false
--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).
List[String] []
--gatk-config-file / NA
A configuration file to use with the GATK.
String null
--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
boolean false
--input / -I
BAM/SAM/CRAM file containing reads
R List[String] []
--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:
- ALL
- OVERLAPPING_ONLY
IntervalMergingRule ALL
--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:
- UNION
- Take the union of all intervals
- INTERSECTION
- Take the intersection of intervals (the subset that overlaps all intervals specified)
IntervalSetRule UNION
--intervals / -L
One or more genomic intervals over which to operate
List[String] []
--lenient / -LE
Lenient processing of VCF files
boolean false
--output / -O
BAM output file
The output SAM/BAM/CRAM file will be written here
R File null
--output-statistics / -os
File to output statistics
If provided, ClipReads will write summary statistics about the clipping operations applied to the reads in this file.
File null
--q-trimming-threshold / -QT
If provided, the Q-score clipper will be applied
If a value > 0 is provided, then the quality score based read clipper will be applied to the reads using this
quality score threshold.
int -1 [ [ -∞ ∞ ] ]
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--read / -read
String null
--read-filter / -RF
Read filters to be applied before analysis
List[String] []
--read-index / -read-index
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.
List[String] []
--read-validation-stringency / -VS
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.
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency SILENT
--reference / -R
Reference sequence
String 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.
String null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR / NA
Undocumented option
List[File] []
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version / NA
display the version number for this tool
boolean false
GATK version 4.0.3.0 built at 02-29-2019 02:29:33.
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