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FixVcfHeader (Picard)

Replaces or fixes a VCF header.This tool will either replace the header in the input VCF file (INPUT) with the given VCF header (HEADER) or will attempt to fill in any field definitions that are missing in the input header by examining the variants in the input VCF file (INPUT). In the latter case, this tool will perform two passes over the input VCF, and any FILTER, INFO, and FORMAT fields found in the VCF records but not found in the input VCF header will be added to the output VCF header with dummy descriptions.

Replace header usage example:

java -jar picard.jar FixVcfHeader \
I=input.vcf \
O=fixed.vcf \
HEADER=header.vcf

Fix header usage example:

java -jar picard.jar FixVcfHeader \
I=input.vcf \
O=fixed.vcf \

Category Variant Manipulation


Overview

Tool for replacing or fixing up a VCF header.

FixVcfHeader (Picard) 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 Arguments
--INPUT
 -I
null The input VCF/BCF file.
--OUTPUT
 -O
null The output VCF/BCF file.
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--CHECK_FIRST_N_RECORDS
 -N
-1 Check only the first N records when searching for missing INFO and FORMAT fields.
--ENFORCE_SAME_SAMPLES
true Enforce that the samples are the same (and in the same order) when replacing the VCF header.
--HEADER
 -H
null The replacement VCF header.
--help
 -h
false display the help message
--version
false display the version number for this tool
Optional Common Arguments
--COMPRESSION_LEVEL
5 Compression level for all compressed files created (e.g. BAM and VCF).
--CREATE_INDEX
false Whether to create a BAM index when writing a coordinate-sorted BAM file.
--CREATE_MD5_FILE
false Whether to create an MD5 digest for any BAM or FASTQ files created.
--GA4GH_CLIENT_SECRETS
client_secrets.json Google Genomics API client_secrets.json file path.
--MAX_RECORDS_IN_RAM
500000 When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
--QUIET
false Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
--TMP_DIR
[] One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER
 -use_jdk_deflater
false Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER
 -use_jdk_inflater
false Use the JDK Inflater instead of the Intel Inflater for reading compressed input
--VALIDATION_STRINGENCY
STRICT Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--VERBOSITY
INFO Control verbosity of logging.
Advanced Arguments
--showHidden
false display hidden arguments

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.


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--CHECK_FIRST_N_RECORDS / -N

Check only the first N records when searching for missing INFO and FORMAT fields.

int  -1  [ [ -∞  ∞ ] ]


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--ENFORCE_SAME_SAMPLES / NA

Enforce that the samples are the same (and in the same order) when replacing the VCF header.

boolean  true


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--HEADER / -H

The replacement VCF header.

File  null


--help / -h

display the help message

boolean  false


--INPUT / -I

The input VCF/BCF file.

R File  null


--MAX_RECORDS_IN_RAM / NA

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]


--OUTPUT / -O

The output VCF/BCF file.

R File  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []


--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false


--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false


--VALIDATION_STRINGENCY / NA

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  STRICT


--VERBOSITY / NA

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR
WARNING
INFO
DEBUG

LogLevel  INFO


--version / NA

display the version number for this tool

boolean  false


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GATK version 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.