Selects headers from a VCF source
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).
A set of VCFs.
A VCF with the selected headers.
java -jar GenomeAnalysisTK.jar \ -T SelectHeaders \ -R reference.fasta \ -V input.vcf \ -o output.vcf \ -hn FILTER \ -hn FORMAT \ -hn INFO
java -jar GenomeAnalysisTK.jar \ -T SelectHeaders \ -R reference.fasta \ -V input.vcf \ -o output.vcf \ -hn FILTER \ -hn FORMAT \ -hn INFO \ -irn \ -iln
java -jar GenomeAnalysisTK.jar \ -T SelectHeaders \ -R reference.fasta \ -V input.vcf \ -o output.vcf \ -hn FILTER \ -hn FORMAT \ -hn INFO \ -he '.*SnpEff.*'
These Read Filters are automatically applied to the data by the Engine before processing by SelectHeaders.
This tool can be run in multi-threaded mode using this option.
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 | |
|---|---|---|---|
| Required Inputs | |||
| --variant -V |
NA | Input VCF file | |
| Optional Outputs | |||
| --out -o |
stdout | File to which variants should be written | |
| Optional Parameters | |||
| --exclude_header_name -xl_hn |
NA | Exclude header. Can be specified multiple times | |
| --header_expression -he |
NA | Regular expression to select many headers from the tracks provided. Can be specified multiple times | |
| --header_name -hn |
NA | Include header. Can be specified multiple times | |
| Optional Flags | |||
| --include_interval_names -iln |
false | If set the interval file name minus the file extension, or the command line intervals, will be added to the headers | |
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. 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.
Set[String] NA
Regular expression to select many headers from the tracks provided. Can be specified multiple times
Set[String] NA
Include header. Can be specified multiple times
Set[String] NA
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.
boolean false
File to which variants should be written
VariantContextWriter stdout
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).
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R RodBinding[VariantContext] NA