SelectHeaders

Selects headers from a VCF source.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

Often, a VCF containing many headers will need to be subset in order to facilitate certain formatting guidelines. SelectHeaders can be used for this purpose. Given a single VCF file, one or more headers can be extracted from the file (based on a complete header name or a pattern match).

Input

A set of VCFs.

Output

A header selected VCF.

Examples

 Select only the FILTER, FORMAT, and INFO headers:
 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T SelectHeaders \
   --variant input.vcf \
   -o output.vcf \
   -hn FILTER \
   -hn FORMAT \
   -hn INFO

 Select only the FILTER, FORMAT, and INFO headers and add in the reference file names:
 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T SelectHeaders \
   --variant input.vcf \
   -o output.vcf \
   -hn FILTER \
   -hn FORMAT \
   -hn INFO \
   -irn \
   -iln

 Select only the FILTER, FORMAT, and INFO headers, plus any headers with SnpEff:
 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T SelectHeaders \
   --variant input.vcf \
   -o output.vcf \
   -hn FILTER \
   -hn FORMAT \
   -hn INFO \
   -he '.*SnpEff.*'

Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using this option.

TreeReducible (-nt)

Command-line Arguments

Inherited arguments

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).

CommandLineGATK

SelectHeaders specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--variant	RodBinding[VariantContext]	NA	Input VCF file
Optional
--exclude_header_name	Set[String]	NA	Exclude header. Can be specified multiple times
--header_expression	Set[String]	NA	Regular expression to select many headers from the tracks provided. Can be specified multiple times
--header_name	Set[String]	NA	Include header. Can be specified multiple times
--include_interval_names	boolean	false	If set the interval file name minus the file extension, or the command line intervals, will be added to the headers
--out	VariantContextWriter	stdout	File to which variants should be written

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.

--exclude_header_name / -xl_hn ( Set[String] )

Exclude header. Can be specified multiple times. Note that header exclusion takes precedence over inclusion, so that if a header is in both lists it will be excluded.

--header_expression / -he ( Set[String] )

Regular expression to select many headers from the tracks provided. Can be specified multiple times.

--header_name / -hn ( Set[String] )

Include header. Can be specified multiple times.

--include_interval_names / -iln ( boolean with default value false )

If set the interval file name minus the file extension, or the command line intervals, will be added to the headers. Note that interval name inclusion takes precedence over other header matching. If set other interval lines may be excluded but the intervals will still be added.

--out / -o ( VariantContextWriter with default value stdout )

File to which variants should be written.

--variant / -V ( required RodBinding[VariantContext] )

Input VCF file. Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file). --variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.