MergeVcfs (picard 2.8.1 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.vcf.MergeVcfs

```
public class MergeVcfs
extends CommandLineProgram
```
Combines multiple VCF files into a single file. Input files must be sorted by their contigs and, within contigs, by start position. Throws IllegalArgumentException if the contig lists are not present in the input files, are not identical or if the sample lists are not the same; this class uses the GATK to merge headers, which may throw exceptions if the headers cannot be merged. See VCFUtils.smartMergeHeaders for details.
An index file is created for the output file by default. Using an output file name with a ".gz" extension will create gzip-compressed output.

Field Summary

Fields
Modifier and Type Field Description

List<File> INPUT

File OUTPUT

File SEQUENCE_DICTIONARY
- Fields inherited from class picard.cmdline.CommandLineProgram
  COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Fields
Modifier and Type	Field	Description
`List<File>`	`INPUT`
`File`	`OUTPUT`
`File`	`SEQUENCE_DICTIONARY`

Constructor Summary

Constructors
Constructor Description

MergeVcfs()

Constructors
Constructor	Description
`MergeVcfs()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`doWork()`	Do the work after command line has been parsed.
`static void`	`main(String[] argv)`

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Option(shortName="I",
        doc="VCF or BCF input files File format is determined by file extension.",
        minElements=1)
public List<File> INPUT

OUTPUT

@Option(shortName="O",
        doc="The merged VCF or BCF file. File format is determined by file extension.")
public File OUTPUT

SEQUENCE_DICTIONARY

@Option(shortName="D",
        doc="The index sequence dictionary to use instead of the sequence dictionary in the input file",
        optional=true)
public File SEQUENCE_DICTIONARY

Constructor Detail
- MergeVcfs
```
public MergeVcfs()
```

Method Detail
- main
```
public static void main(String[] argv)
```
- doWork
```
protected int doWork()
```
  Description copied from class: CommandLineProgram
  
  Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
  
  Specified by:
  
  doWork in class CommandLineProgram
  
  Returns:
  
  program exit status.

Class MergeVcfs

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

INPUT

OUTPUT

SEQUENCE_DICTIONARY

Constructor Detail

MergeVcfs

Method Detail

main

doWork