Generates table of filtered base counts at het sites for allele specific expression
Category Coverage Analysis
OverviewCalculate 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.
- BAM files (with proper headers) to be analyzed for ASE
- A VCF file with specific sites to process.
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.
gatk ASEReadCounter \ -R Homo_sapiens_assembly38.fasta \ -I input.bam \ -V sites.vcf.gz \ -O output.table
- 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.
- 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.
These Read Filters are automatically applied to the data by the Engine before processing by ASEReadCounter.
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|
|||BAM/SAM/CRAM file containing reads|
|||One or more VCF files|
|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).|
|COUNT_FRAGMENTS_REQUIRE_SAME_BASE||Handling of overlapping reads from the same fragment|
|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!|
|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.|
|false||display the help message|
|ALL||Interval merging rule for abutting intervals|
|||One or more genomic intervals over which to operate|
||0||Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.|
|0||Minimum base quality|
|-1||Minimum number of bases that pass filters|
|0||Minimum read mapping quality|
|null||Output file (if not provided, defaults to STDOUT)|
||RTABLE||Format of the output file|
||false||If true, don't emit genotype fields when writing vcf file output.|
||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|
||null||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|
||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|
||null||Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.|
||null||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.|
||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.
--arguments_file / NA
read one or more arguments files and add them to the command line
--cloud-index-prefetch-buffer / -CIPB
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
--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 all reads independently (even if from the same fragment).
- Count all fragments (even if the reads that compose the fragment are not consistent at that base).
- Count all fragments (but only if the reads that compose the fragment are consistent at that base).
--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
--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
--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).
--gatk-config-file / NA
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 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help / -h
display the help message
--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:
--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-depth-per-sample / -max-depth-per-sample
Maximum number of reads to retain per sample per locus. Reads above this threshold will be downsampled. Set to 0 to disable.
int 0 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--output / -O
Output file (if not provided, defaults to STDOUT)
--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:
--QUIET / NA
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:
--reference / -R
--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.
--tmp-dir / NA
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)
--variant / -V
One or more VCF files
R List[FeatureInput[VariantContext]] 
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
--version / NA
display the version number for this tool
GATK version 220.127.116.11 built at Thu, 5 Dec 2019 09:51:56 -0500.