Combines multiple variant files into a single variant file.
Inputs
- One or more input file in VCF format (can be gzipped, i.e. ending in ".vcf.gz", or binary compressed, i.e. ending in ".bcf").
- Optionally a sequence dictionary file (typically name ending in .dict) if the input VCF does not contain a complete contig list and if the output index is to be created (true by default).
The input variant data must adhere to the following rules:
- If there are samples, those must be the same across all input files.
- Input file headers must be contain compatible declarations for common annotations (INFO, FORMAT fields) and filters.
- Input files variant records must be sorted by their contig and position following the sequence dictionary provided or the header contig list.
You can either directly specify the list of files by specifying INPUT
multiple times, or provide a list in a file with name ending in ".list" to INPUT
.
Outputs
A VCF sorted (i) according to the dictionary and (ii) by coordinate.
Usage examples
Example 1:
We combine several variant files in different formats, where at least one of them contains the contig list in its header.
java -jar picard.jar MergeVcfs \ I=input_variants.01.vcf \ I=input_variants.02.vcf.gz \ O=output_variants.vcf.gz
Example 2:
Similar to example 1 but we use an input list file to specify the input files:
java -jar picard.jar MergeVcfs \ I=input_variant_files.list \ O=output_variants.vcf.gz
Category Variant Manipulation
Overview
Combines multiple variant files into a single variant file.Inputs
- One or more input file in VCF format (can be gzipped, i.e. ending in ".vcf.gz", or binary compressed, i.e. ending in ".bcf").
- Optionally a sequence dictionary file (typically name ending in .dict) if the input VCF does not contain a complete contig list and if the output index is to be created (true by default).
The input variant data must adhere to the following rules:
- If there are samples, those must be the same across all input files.
- Input file headers must be contain compatible declarations for common annotations (INFO, FORMAT fields) and filters.
- Input files variant records must be sorted by their contig and position following the sequence dictionary provided or the header contig list.
You can either directly specify the list of files by specifying INPUT
multiple times, or provide a list
in a file with name ending in ".list" to INPUT
.
Outputs
A VCF sorted (i) according to the dictionary and (ii) by coordiante.Usage examples
Example 1:
We combine several variant files in different formats, where at least one of them contains the contig list in its header.java -jar picard.jar MergeVcfs \ I=input_variants.01.vcf \ I=input_variants.02.vcf.gz \ O=output_variants.vcf.gz
Example 2:
Similar to example 1 but we use an input list file to specify the input files:java -jar picard.jar MergeVcfs \ I=input_variant_files.list \ O=output_variants.vcf.gz
MergeVcfs (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 |
VCF or BCF input files (File format is determined by file extension), or a file having a '.list' suffix containing the path to the files, one per line. | ||
--OUTPUT -O |
The merged VCF or BCF file. File format is determined by file extension. | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--COMMENT -CO |
Comment(s) to include in the merged output file's header. | ||
--help -h |
false | display the help message | |
--SEQUENCE_DICTIONARY -D |
The index sequence dictionary to use instead of the sequence dictionary in the input files | ||
--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 |
true | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
--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 |
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
read one or more arguments files and add them to the command line
List[File] []
--COMMENT / -CO
Comment(s) to include in the merged output file's header.
List[String] []
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean true
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INPUT / -I
VCF or BCF input files (File format is determined by file extension), or a file having a '.list' suffix containing the path to the files, one per line.
R List[File] []
--MAX_RECORDS_IN_RAM
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 merged VCF or BCF file. File format is determined by file extension.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--SEQUENCE_DICTIONARY / -D
The index sequence dictionary to use instead of the sequence dictionary in the input files
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR
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
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
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
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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