Sort a VCF a field in the INFO column
Usage: sortvcfoninfo [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
--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].
--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
* -T, --tag, -t
INFO tag. Special words are '<ID>' to sort on ID, and <QUAL> to sort on
QUAL
--tmpDir
tmp working directory. Default: java.io.tmpDir
Default: []
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sortvcfoninfo
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite sortvcfoninfo ? 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
##Example
]$ curl "https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf" |\
java -jar dist/sortvcfoninfo.jar -F BaseQRankSum | grep -vE "^#"
chr10 1142208 . T C 3404.30 . AC=8;AF=1.00;AN=8;
chr10 135336656 . G A 38.34 . AC=4;AF=1.00;AN=4;
chr10 52004315 . T C 40.11 . AC=4;AF=1.00;AN=4;
chr10 52497529 . G C 33.61 . AC=4;AF=1.00;AN=4;
chr10 126678092 . G A 89.08 . AC=1;AF=0.13;AN=8;BaseQRankSum=-3.120;
chr16 72057435 . C T 572.98 . AC=1;AF=0.13;AN=8;BaseQRankSum=-2.270;
chr10 48003992 . C T 1047.87 . AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;
chr10 135210791 . T C 65.41 . AC=4;AF=0.50;AN=8;BaseQRankSum=2.054;
chr10 135369532 . T C 122.62 . AC=2;AF=0.25;AN=8;BaseQRankSum=2.118;