Emulates the samtools pileup command to print aligned reads
Prints the alignment in something similar to the samtools pileup format. Each line represents a genomic position,
consisting of chromosome name, coordinate, reference base, read bases, and read qualities.
Emulated command:
samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate]
A BAM file and the interval to print.
Formatted pileup-style alignment of reads.
These Read Filters are automatically applied to the data by the Engine before processing by Pileup. This tool can be run in multi-threaded mode using these options. The arguments described in the entries below can be supplied to this tool to modify
its behavior. For example, the -L argument directs the GATK engine restricts processing
to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers). This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table. 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 these ROD bindings to the output Pileup.
--metadata binds reference ordered data. This argument supports ROD files of the
following types: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, OLDDBSNP, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3
An output file created by the walker. Will overwrite contents if file exists.
Add an extra verbose section to the pileup output. In addition to the standard pileup output, adds 'verbose' output too. The verbose output contains the number of spanning deletions,
and for each read in the pileup it has the read name, offset in the base string, read length, and read mapping quality. These per
read items are delimited with an '@' character.
See also
Guide Index |
Technical Documentation Index |
Support Forum
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.Input
Output
Example
java -Xmx2g -jar GenomeAnalysisTK.jar \
-T Pileup \
-R ref.fasta \
-I aligned_reads.bam \
-o output.txt
Additional Information
Read filters
Parallelism options
Command-line Arguments
Inherited arguments
Pileup specific arguments
Name
Type
Default value
Summary
Optional
--metadata
List[RodBinding[Feature]]
[]
Add these ROD bindings to the output Pileup
--out
PrintStream
stdout
An output file created by the walker. Will overwrite contents if file exists
--showVerbose
boolean
false
Add an extra verbose section to the pileup output
Argument details
--metadata
/ -metadata
(
List[RodBinding[Feature]]
with default value []
)
--out
/ -o
(
PrintStream
with default value stdout
)
--showVerbose
/ -verbose
(
boolean
with default value false
)
