jvarkit
VCFMerge
Merge a large number of VCF Files
Usage
Usage: vcfmerge [options] Files
Options:
--bcf-output
If this program writes a VCF to a file, The format is first guessed from
the file suffix. Otherwise, force BCF output. The current supported BCF
version is : 2.1 which is not compatible with bcftools/htslib (last
checked 2019-11-15)
Default: false
--fields
print the following INFO/FORMAT Fields.
Default: AC,AN,AF,DP,GQ,AD,PL
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-homref, --homref, -hr
Use HomRef 0/0 for unknown variant
Default: false
--maxRecordsInRam
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 a file, and increases
the amount of RAM needed
Default: 50000
-o, --output
Output file. Optional . Default: stdout
--ploidy
Ploidy
Default: 2
-region, --region, -r
Merge in that region: An interval as the following syntax :
"chrom:start-end" or "chrom:middle+extend" or "chrom:start-end+extend"
or "chrom:start-end+extend-percent%".A program might use a Reference
sequence to fix the chromosome name (e.g: 1->chr1)
Default: <empty string>
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--version
print version and exit
Keywords
- vcf
- sort
- merge
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfmerge
The java jar file will be installed in the dist directory.
Creation Date
20130916
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite vcfmerge ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
The motivation for this is to merge a large number of VCF files without opening a bunch of temporary files.
For a regular normal number of files you should use GATK combineVariants or bcftools merge
Example
$ java -jar dist/vcfmerge.jar -hr src/test/resources/S*.vcf.gz | more
[INFO][VCFMerge]merging...5 vcfs
##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4 S5
RF01 970 . A C . . AC=2;AF=0.200;AN=10 GT 0/0 0/0 0/0 0/0 1/1
RF01 3246 . A G . . AC=2;AF=0.200;AN=10 GT 0/0 0/0 0/0 0/0 1/1
RF02 578 . G A . . AC=2;AF=0.200;AN=10 GT 0/0 0/0 0/0 1/1 0/0
RF02 877 . T A . . AC=1;AF=0.100;AN=10 GT 0/1 0/0 0/0 0/0 0/0
RF02 1962 . TACA TA . . AC=1;AF=0.100;AN=10 GT 0/1 0/0 0/0 0/0 0/0
RF02 2332 . AT A . . AC=1;AF=0.100;AN=10 GT 0/0 0/0 0/0 0/1 0/0
RF02 2662 . G C . . AC=2;AF=0.200;AN=10 GT 0/0 0/0 0/0 0/0 1/1