jvarkit
VcfCadd
Annotate VCF with Combined Annotation Dependent Depletion (CADD) (Kircher & al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892.PubMed PMID: 24487276.
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcfcadd [options] Files
Usage: vcfcadd [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
-d, --buffer-size
Buffer size / processing window size. 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
--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].
-o, --out
Output file. Optional . Default: stdout
* -u, --uri, --tabix, --cadd
Combined Annotation Dependent Depletion (CADD) Tabix file URI
Default: <empty string>
--version
print version and exit
-na
value used for 'allele-not-found'.
Default: -999.0
Keywords
- vcf
- prediction
- cadd
- annotation
Creation Date
20220119
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 vcfcadd ? 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 -Dhttp.proxyHost=my.proxy.host.fr -Dhttp.proxyPort=1234 -jar dist/jvarkit.jar vcfcadd \
-u "http://krishna.gs.washington.edu/download/CADD/v1.3/1000G_phase3.tsv.gz" \
src/test/resources/gnomad.exomes.r2.0.1.sites.vcf.gz 2> /dev/null | ~/package/bcftools/bcftools annotate -x '^INFO/CADD_SCORE,INFO/CADD_PHRED'
##fileformat=VCFv4.2
(...)
##INFO=<ID=CADD_PHRED,Number=A,Type=Float,Description="PHRED expressing the rank in order of magnitude terms. For example, reference genome single nucleotide variants at the 10th-% of CADD scores are assigned to CADD-10, top 1% to CADD-20, top 0.1% to CADD-30, etc. URI was http://krishna.gs.washington.edu/download/CADD/v1.3/1000G_phase3.tsv.gz">
##INFO=<ID=CADD_SCORE,Number=A,Type=Float,Description="Score suggests that that variant is likely to be observed (negative values) vs simulated(positive values).However, raw values do have relative meaning, with higher values indicating that a variant is more likely to be simulated (or -not observed-) and therefore more likely to have deleterious effects. URI was http://krishna.gs.washington.edu/download/CADD/v1.3/1000G_phase3.tsv.gz">
##VcfCaddCmdLine=-u http://krishna.gs.washington.edu/download/CADD/v1.3/1000G_phase3.tsv.gz src/test/resources/gnomad.exomes.r2.0.1.sites.vcf.gz
(...)
#CHROM POS ID REF ALT QUAL FILTER INFO
1 905606 rs540662886 G C,A 41743.9 PASS CADD_PHRED=3.426,.;CADD_SCORE=0.082875,.
(...)
1 905621 rs368876607 G A 14291.5 PASS CADD_PHRED=6.025;CADD_SCORE=0.334762
(...)
1 905669 rs111483874 C G,T 86574.3 PASS CADD_PHRED=12.77,.;CADD_SCORE=1.39614,.
(...)
1 905723 rs150703609 G A 15622.1 PASS CADD_PHRED=23.7;CADD_SCORE=4.05532
1 905726 rs751084833 C T,A 8733.36 PASS .
1 905727 rs761609807 G A 12936.9 PASS .
(..)
Note to self
I got problem with the certificate. Fixed with -Dcom.sun.security.enableAIAcaIssuers=true -Dcom.sun.net.ssl.checkRevocation=false