Showing docs for version 3.7-0

ASEReadCounter

Calculate read counts per allele for allele-specific expression analysis

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

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.

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

 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]

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 "-drf DuplicateRead" flag in the command-line.

Caveat

This tool will only process biallelic 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".

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by ASEReadCounter.

Downsampling settings

This tool applies the following downsampling settings by default.

Mode: BY_SAMPLE
To coverage: 10,000

Command-line Arguments

Engine arguments

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.

CommandLineGATK

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 Inputs
--sitesVCFFile -sites	NA	Undocumented option
Optional Outputs
--out -o	stdout	An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--countOverlapReadsType -overlap	COUNT_FRAGMENTS_REQUIRE_SAME_BASE	Handling of overlapping reads from the same fragment
--minBaseQuality -mbq	0	Minimum base quality
--minDepthOfNonFilteredBase -minDepth	-1	Minimum number of bases that pass filters
--minMappingQuality -mmq	0	Minimum read mapping quality
--outputFormat	RTABLE	Format of the output file, can be CSV, TABLE, RTABLE

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.

--countOverlapReadsType / -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 --countOverlapReadsType 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

--minBaseQuality / -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 [ [ -1 127 ] ]

--minDepthOfNonFilteredBase / -minDepth

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 ] ]

--minMappingQuality / -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 [ [ -1 2,147,483,647 ] ]

--out / -o

An output file created by the walker. Will overwrite contents if file exists

PrintStream stdout

--outputFormat / NA

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:

TABLE
RTABLE
CSV

OUTPUT_FORMAT RTABLE

--sitesVCFFile / -sites

Undocumented option

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext] NA