jvarkit
VcfROH
VCF ROH
Usage
Usage: vcfroh [options] Files
Options:
--bed
Output BED instead of interval list
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--min-length
Minimum block length. A distance specified as a positive integer.Commas
are removed. The following suffixes are interpreted :
b,bp,k,kb,m,mb,g,gb
Default: 1000
--min-score
Minimum block score.
Default: 0.0
--min-variants
Minimum number of variants.
Default: 10
--nc2hr
treat NO_CALL to HOM_REF
Default: false
--output, -o
Output file. Optional . Default: stdout
--regions-file
Limit to intervals overlapping that BED file.
--score
HOM_REF/HOM_VAR score. HET score will be 'x' - 1.0.
Default: 0.0025
--version
print version and exit
Keywords
- vcf
- roh
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 vcfroh
The java jar file will be installed in the dist directory.
Creation Date
20211123
Source code
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 vcfroh ? 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
java -jar dist/vcfpar.jar in.vcf > out.vcf