Pileup

Print read alignments in Pileup-style format

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

This tool emulates the 'samtools pileup' command. It prints the alignment in a format that is very similar to the Samtools pileup format (see the Pileup format documentation for more details about the original format). There is one line per genomic position, listing the chromosome name, coordinate, reference base, read bases, and read qualities. In addition to these default fields, additional information can be added to the output as extra columns; see options detailed below.

Emulated command:

  samtools pileup -f in.ref.fasta -l in.site_list input.bam
 

Input

A BAM file and the interval to print.

Output

Alignment of reads formatted in the Pileup style.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T Pileup \
   -R reference.fasta \
   -I my_reads.bam \
   -L chr1:257-267
   -o output.txt
 

Expected output

     chr1 257 A CAA '&=
     chr1 258 C TCC A:=
     chr1 259 C CCC )A=
     chr1 260 C ACC (=<
     chr1 261 T TCT '44
     chr1 262 A AAA '?:
     chr1 263 A AGA 1'6
     chr1 264 C TCC 987
     chr1 265 C CCC (@(
     chr1 266 C GCC ''=
     chr1 267 T AAT 7%>
 

Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using these options.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

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.

Pileup 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
Optional Inputs
--metadata
[] ROD file containing metadata
Optional Outputs
--out
 -o
stdout An output file created by the walker. Will overwrite contents if file exists
Optional Flags
--showVerbose
 -verbose
false Add an extra verbose section to the pileup output

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.


--metadata / -metadata

ROD file containing metadata
This enables annotating the pileup to show overlaps with metadata from a ROD file. For example, if you provide a VCF and there is a SNP at a given location covered by the pileup, the pileup output at that position will be annotated with the corresponding source ROD identifier.

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

List[RodBinding[Feature]]  []


--out / -o

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

PrintStream  stdout


--showVerbose / -verbose

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.

boolean  false


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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.