Generates table of filtered base counts at het sites for allele specific expression

Category Coverage Analysis

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Overview

Calculate read counts per allele for allele-specific expression analysis of RNAseq data

This tool calculates allele counts at a set of positions after applying filters that are tuned for enabling allele-specific expression (ASE) analysis of RNAseq data. The filters operate on mapping quality, base quality, depth of coverage, overlapping paired reads and deletions overlapping the position. All thresholds and options are controlled by command-line arguments.

Input

• BAM files (with proper headers) to be analyzed for ASE
• A VCF file with specific sites to process.

Output

A table of allele counts at the given sites. By default, it is formatted as a tab-delimited text file that is readable by R and compatible with Mamba, a downstream tool developed for allele-specific expression analysis.

Usage Example

gatk ASEReadCounter \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -V sites.vcf.gz \ -O output.table

Note

• Like most GATK tools, this tools filters out duplicate reads by default. However, some ASE methods recommend including duplicate reads in the analysis, so the DuplicateRead filter can be disabled using the "-DF NotDuplicateReadFilter" flag in the command-line.

Caveat

• This tool will only process biallelic het SNP sites. If your callset contains multiallelic sites, they will be ignored. Optionally, you can subset your callset to just biallelic variants using e.g. SelectVariants with the option "-restrictAllelesTo BIALLELIC".

For more details see Castel, S. et al. Tools and Best Practices for allelic expression analysis.

ASEReadCounter 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
--variant  -V	[]	One or more VCF files
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).
--count-overlap-reads-handling  -overlap	COUNT_FRAGMENTS_REQUIRE_SAME_BASE	Handling of overlapping reads from the same fragment
--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!
--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
--maxDepthPerSample	0	Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.
--min-base-quality  -mbq	0	Minimum base quality
--min-depth-of-non-filtered-base  -min-depth	-1	Minimum number of bases that pass filters
--min-mapping-quality  -mmq	0	Minimum read mapping quality
--output  -O	null	Output file (if not provided, defaults to STDOUT)
--output-format	RTABLE	Format of the output file
--reference  -R	null	Reference sequence
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--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.
--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.

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--add-output-sam-program-record / -add-output-sam-program-record

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean  true

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--add-output-vcf-command-line / -add-output-vcf-command-line

If true, adds a command line header line to created VCF files.

boolean  true

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--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []

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--cloud-index-prefetch-buffer / -CIPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int  -1  [ [ -∞  ∞ ] ]

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--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  40  [ [ -∞  ∞ ] ]

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--count-overlap-reads-handling / -overlap

Handling of overlapping reads from the same fragment
These options modify how the tool deals with overlapping read pairs. The default value is COUNT_FRAGMENTS_REQUIRE_SAME_BASE.

The --count-overlap-reads-handling argument is an enumerated type (CountPileupType), which can have one of the following values:

COUNT_READS

Count all reads independently (even if from the same fragment).

COUNT_FRAGMENTS

Count all fragments (even if the reads that compose the fragment are not consistent at that base).

COUNT_FRAGMENTS_REQUIRE_SAME_BASE

Count all fragments (but only if the reads that compose the fragment are consistent at that base).

CountPileupType  COUNT_FRAGMENTS_REQUIRE_SAME_BASE

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--create-output-bam-index / -OBI

If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

boolean  true

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--create-output-bam-md5 / -OBM

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean  false

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--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true

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--create-output-variant-md5 / -OVM

If true, create a a MD5 digest any VCF file created.

boolean  false

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--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

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--disable-read-filter / -DF

Read filters to be disabled before analysis

List[String]  []

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--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

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--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

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--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]  []

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--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

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--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  [ [ -∞  ∞ ] ]

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--help / -h

display the help message

boolean  false

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--input / -I

BAM/SAM/CRAM file containing reads

R List[String]  []

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--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  [ [ -∞  ∞ ] ]

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--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

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--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  [ [ -∞  ∞ ] ]

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--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

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--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

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--lenient / -LE

Lenient processing of VCF files

boolean  false

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--maxDepthPerSample / -maxDepthPerSample

Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.

int  0  [ [ -∞  ∞ ] ]

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--min-base-quality / -mbq

Minimum base quality
If this argument is enabled, bases with quality scores lower than this threshold will not be counted. This can be set to -1 by default to disable the evaluation and ignore this threshold.

byte  0  [ [ -∞  ∞ ] ]

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--min-depth-of-non-filtered-base / -min-depth

Minimum number of bases that pass filters
If this argument is enabled, loci with total depth lower than this threshold after all filters have been applied will be skipped. This can be set to -1 by default to disable the evaluation and ignore this threshold.

int  -1  [ [ -∞  ∞ ] ]

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--min-mapping-quality / -mmq

Minimum read mapping quality
If this argument is enabled, reads with mapping quality values lower than this threshold will not be counted. This can be set to -1 by default to disable the evaluation and ignore this threshold.

int  0  [ [ -∞  ∞ ] ]

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--output / -O

Output file (if not provided, defaults to STDOUT)

File  null

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--output-format / NA

Format of the output file
Available options are csv, table, rtable. By default, the format is rtable (an r-readable table).

The --output-format argument is an enumerated type (OUTPUT_FORMAT), which can have one of the following values:

TABLE

RTABLE

CSV

OUTPUT_FORMAT  RTABLE

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--QUIET / NA

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

Boolean  false

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--read-filter / -RF

Read filters to be applied before analysis

List[String]  []

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--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]  []

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--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

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--reference / -R

Reference sequence

String  null

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--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

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--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

String  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--sites-only-vcf-output / NA

If true, don't emit genotype fields when writing vcf file output.

boolean  false

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--TMP_DIR / NA

Undocumented option

List[File]  []

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--variant / -V

One or more VCF files

R List[FeatureInput[VariantContext]]  []

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--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

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--version / NA

display the version number for this tool

boolean  false

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GATK version 4.0.8.1 built at 25-41-2019 10:41:16.