VCFPolyX
Number of repeated REF bases around POS.
Usage
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcfpolyx [options] Files
Usage: vcfpolyx [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].
-n, --filter, --max-repeats
if number of repeated bases is greater or equal to 'n' set a FILTER =
(tag)
Default: -1
-o, --out
Output file. Optional . Default: stdout
* -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard/gatk CreateSequenceDictionary or samtools dict
--skip-filtered
Don't spend some time to calculate the tag if the variant is FILTERed
Default: false
-t, --tag
Tag used in INFO and FILTER columns.
Default: POLYX
--version
print version and exit
Keywords
- vcf
- repeat
Creation Date
20200930
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 vcfpolyx ? 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/vcfpolyx.jar -R reference.fa input.vcf
(...)
2 1133956 . A G 2468.84 . POLYX=23
2 1133956 . A AG 3604.25 . POLYX=23
2 2981671 . T G 47.18 . POLYX=24
(...)
Cited in:
- "Multiscale heterogeneity in gastric adenocarcinomaevolution is an obstacle to precision medicine" https://assets.researchsquare.com/files/rs-62554/v1/7883b5d6-a5e6-4d39-8554-e9fef719ac42.pdf
- Maitena Tellaetxe-Abete, Borja Calvo, Charles Lawrie, Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data, NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab092, https://doi.org/10.1093/nargab/lqab092
- Pol32, an accessory subunit of DNA polymerase delta, plays an essential role in genome stability and pathogenesis of Candida albicans. Shraddheya Kumar Patel & al. Gut Microbes. https://doi.org/10.1080/19490976.2022.2163840 2023.
- Heczko, L., Hlavac, V., Holy, P. et al. Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases. Cancer Cell Int 23, 295 (2023). https://doi.org/10.1186/s12935-023-03135-x