Calculate read counts per allele for allele-specific expression analysis
This tool calculates allele counts at a set of positions after applying filters that are tuned for enabling allele-specific expression (ASE) analysis. 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.
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.
java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T ASEReadCounter \ -o file_name.csv \ -I input.bam \ -sites sites.vcf \ -U ALLOW_N_CIGAR_READS \ [-minDepth 10] \ [--minMappingQuality 10] \ [--minBaseQuality 2] \ [-drf DuplicateRead]
These Read Filters are automatically applied to the data by the Engine before processing by ASEReadCounter.
This tool applies the following downsampling settings by default.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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|
|stdout||An output file created by the walker. Will overwrite contents if file exists|
|COUNT_FRAGMENTS_REQUIRE_SAME_BASE||Handling of overlapping reads from the same fragment|
|0||Minimum base quality|
|-1||Minimum number of bases that pass filters|
|0||Minimum read mapping quality|
||RTABLE||Format of the output file, can be CSV, TABLE, RTABLE|
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.
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 --countOverlapReadsType argument is an enumerated type (CountPileupType), which can have one of the following values:
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 [ [ -1 127 ] ]
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 [ [ -1 2,147,483,647 ] ]
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 [ [ -1 2,147,483,647 ] ]
An output file created by the walker. Will overwrite contents if file exists
Format of the output file, can be CSV, TABLE, RTABLE
Available options are csv, table, rtable. By default, the format is rtable (an r-readable table).
The --outputFormat argument is an enumerated type (OUTPUT_FORMAT), which can have one of the following values:
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R RodBinding[VariantContext] NA
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.