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PrintReadsContaining

Print read pairs matching a list of sequences/expressions

Category Public/Stable Tools

Overview

This walker will iterate FASTQ or pair of FASTQs and print any reads matching the supplied expressions. Expressions can be simple strings or a java regular expression.

Usage examples:

Simple search for a sequence in either forward or reverse read:

  java -jar DISCVRseq.jar PrintReadsContaining \
     -FQ fastq_R1.fastq.gz \
     -FQ2 fastq_R2.fastq.gz \
     -e 'TACG' \
     -O output_R1.fastq.gz \
     -O2 output_R2.fastq.gz

RegEx search for reads where either forward or reverse contains only A/T

  java -jar DISCVRseq.jar PrintReadsContaining \
     -FQ fastq_R1.fastq.gz \
     -FQ2 fastq_R2.fastq.gz \
     -e '^[AT]+$ \
     -O output_R1.fastq.gz \
     -O2 output_R2.fastq.gz

Same as above, except tests forward read only

  java -jar DISCVRseq.jar PrintReadsContaining \
     -FQ fastq_R1.fastq.gz \
     -FQ2 fastq_R2.fastq.gz \
     -e1 '^[AT]+$' \
     -O output_R1.fastq.gz \
     -O2 output_R2.fastq.gz

In this example, the forward read must be exclusively A/T, and either the forward or reverse must contain AA

  java -jar DISCVRseq.jar PrintReadsContaining \
     -FQ fastq_R1.fastq.gz \
     -FQ2 fastq_R2.fastq.gz \
     -e1 '^[AT]+$' \
     -e 'AA' \
     -O output_R1.fastq.gz \
     -O2 output_R2.fastq.gz

In this example, one of these two conditions must be true: either read is exclusively A/T or either read contains AA

  java -jar DISCVRseq.jar PrintReadsContaining \
     -FQ fastq_R1.fastq.gz \
     -FQ2 fastq_R2.fastq.gz \
     -e '^[AT]+$' \
     -e 'AA' \
     -O output_R1.fastq.gz \
     -O2 output_R2.fastq.gz

Similar to the above, except both conditions must be met.

  java -jar DISCVRseq.jar PrintReadsContaining \
     -FQ fastq_R1.fastq.gz \
     -FQ2 fastq_R2.fastq.gz \
     -e '^[AT]+$' \
     -e 'AA' \
     --matchAllExpressions \
     -O output_R1.fastq.gz \
     -O2 output_R2.fastq.gz

Additional Information

Genome/Reference Files

Please note that if this tools uses a reference genome, that FASTA must be indexed with samtools and to have a sequence dictionary created with Picard. See here for more information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by PrintReadsContaining.

WellformedReadFilter

PrintReadsContaining 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
--fastq	null	Input fastq file (optionally gzipped) for single end data, or first read in paired end data.
--output	null	The output file for the first FASTQ file
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--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).
--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.
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--editDistance -ed	0	If provided, all expressions will be treated as simple strings, and must be ATGC characters. The tool will scan each motif against the read(s) and report a match if the edit distance is less than or equal to this threshold.
--expressionNames -en	[]	A mechanism to allow names for each expression. If used, the number of expression names (-en) must be equal to the number of expressions (-e). If not provided, the expression itself will be used.
--expressions -e	[]	A list of sequences or regular expressions to test. If either the forward or reverse read matches, it will be included.
--fastq2	null	Input fastq file (optionally gzipped) for the second read of paired end data.
--gcs-max-retries -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays	""	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.
--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
--matchAllExpressions -ma	false	If provided, a read pair must match all sequences/expressions to be included. Default: false
--output2	null	The output file for the second FASTQ file. Required if -FQ2 is used.
--read1ExpressionNames -e1n	[]	A mechanism to allow names for each read1 expression. If used, the number of read1 expression names (-e1n) must be equal to the number of read1 expressions (-e1). If not provided, the expression itself will be used.
--read1Expressions -e1	[]	A list of sequences or regular expressions to test against the forward read. If passing, the pair will be included.
--read2ExpressionNames -e2n	[]	A mechanism to allow names for each read2 expression. If used, the number of read2 expression names (-e2n) must be equal to the number of read2 expressions (-e2). If not provided, the expression itself will be used.
--read2Expressions -e2	[]	A list of sequences or regular expressions to test against the reverse read. If passing, the pair will be included.
--reference -R	null	Reference sequence
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--summaryFile	null	If provided, a TSV summary of matches will be written here.
--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-tool-default-read-filters	false	Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
--exclude-intervals -XL	[]	One or more genomic intervals to exclude from processing
--gatk-config-file	null	A configuration file to use with the GATK.
--input -I	[]	BAM/SAM/CRAM file containing reads
--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
--max-variants-per-shard	0	If non-zero, partitions VCF output into shards, each containing up to the given number of records.
--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	null	Temp directory to use.
--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] []

--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

--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 (WARNING: many tools will not function correctly without their default read filters on)

boolean false

--editDistance / -ed

If provided, all expressions will be treated as simple strings, and must be ATGC characters. The tool will scan each motif against the read(s) and report a match if the edit distance is less than or equal to this threshold.

int 0 [ [ -∞ ∞ ] ]

--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). strings gathered from the command line -XL argument to be parsed into intervals to exclude

List[String] []

--expressionNames / -en

A mechanism to allow names for each expression. If used, the number of expression names (-en) must be equal to the number of expressions (-e). If not provided, the expression itself will be used.

List[String] []

--expressions / -e

A list of sequences or regular expressions to test. If either the forward or reverse read matches, it will be included.

List[String] []

--fastq / NA

Input fastq file (optionally gzipped) for single end data, or first read in paired end data.

R File null

--fastq2 / NA

Input fastq file (optionally gzipped) for the second read of paired end data.

File null

--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 [ [ -∞ ∞ ] ]

--gcs-project-for-requester-pays / NA

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.

String ""

--help / -h

display the help message

boolean false

--input / -I

BAM/SAM/CRAM file containing reads

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:

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
INTERSECTION

IntervalSetRule UNION

--intervals / -L

One or more genomic intervals over which to operate

List[String] []

--lenient / -LE

Lenient processing of VCF files

boolean false

--matchAllExpressions / -ma

If provided, a read pair must match all sequences/expressions to be included. Default: false

boolean false

--max-variants-per-shard / NA

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int 0 [ [ 0 ∞ ] ]

--output / NA

The output file for the first FASTQ file

R File null

--output2 / NA

The output file for the second FASTQ file. Required if -FQ2 is used.

File null

--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean false

--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[GATKPath] []

--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

--read1ExpressionNames / -e1n

A mechanism to allow names for each read1 expression. If used, the number of read1 expression names (-e1n) must be equal to the number of read1 expressions (-e1). If not provided, the expression itself will be used.

List[String] []

--read1Expressions / -e1

A list of sequences or regular expressions to test against the forward read. If passing, the pair will be included.

List[String] []

--read2ExpressionNames / -e2n

A mechanism to allow names for each read2 expression. If used, the number of read2 expression names (-e2n) must be equal to the number of read2 expressions (-e2). If not provided, the expression itself will be used.

List[String] []