jvarkit
VcfSpliceAI
Annotate VCF with spiceai web service
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcfspliceai [options] Files
Usage: vcfspliceai [options] Files
Options:
--base
Base API
Default: https://spliceailookup-api.broadinstitute.org/spliceai/
--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
--distance
For each variant, SpliceAI looks within a window (+/- 50bp by default)
to see how the variant affects the probabilities of different positions
being splice acceptors or donors. The distance specified here controls
the size of this window. The maximum allowed value is 10,000bp
Default: 50
--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].
--hg
genome version. Must be 37 or 38. Otherwise, the dictionary is used to
detect the version.
Default: -1
-o, --out
Output file. Optional . Default: stdout
--raw
Splicing changes corresponding to strengthening annotated splice sites
and weakening unannotated splice sites are typically much less
pathogenic than weakening annotated splice sites and strengthening
unannotated splice sites. Selecting 'masked' (default) will hide the
score for such splicing changes and show 0 instead. Selecting 'raw' will
show all scores. SpliceAI developers recommend using 'raw' scores for
alternative splicing analysis and 'masked' scores for variant
interpretation.
Default: false
--tag
INFO tag
Default: SPLICEAI
--version
print version and exit
Keywords
- vcf
- splice
- splicing
- spliceai
Creation Date
20201107
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 vcfspliceai ? 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/jvarkit.jar vcfspliceai src/test/resources/test_vcf01.vcf
(...)
#CHROM POS ID REF ALT QUAL FILTER INFO
(...)
1 866893 . T C 431 PASS AA=t;AC=7;AF=0.7;AN=10;SPLICEAI=SAMD11|0.00|0.00|0.00|0.00|-13|24|-13|-48
1 870317 . G A 12 PASS AC=11;AF=0.917;AN=12;SPLICEAI=SAMD11|0.00|0.00|0.00|0.00|2|17|16|-12
1 875770 . A G 338 PASS AA=a;AC=8;AF=0.8;AN=10;SPLICEAI=SAMD11|0.00|0.00|0.01|0.00|-1|-45|-50|-46
1 903245 . A G 199 PASS AA=a;AC=6;AF=0.6;AN=10;SPLICEAI=PLEKHN1|0.00|0.00|0.00|0.00|48|-37|-22|1
1 905130 . ATG A 487 PASS AC=3;AF=0.5;AN=6;CIGAR=1M2D;IDREP=1;REFREP=2;RU=TG;SPLICEAI=PLEKHN1|0.00|0.00|0.00|0.00|-43|21|-33|-37
1 909238 . G C 229 PASS AA=C;AC=8;AF=0.667;AN=12;SPLICEAI=PLEKHN1|0.00|0.01|0.00|0.00|-43|-50|39|-7
1 912049 . T C 400 PASS AA=T;AC=5;AF=0.625;AN=8;SPLICEAI=PERM1|0.00|0.01|0.01|0.00|-28|-14|-27|-23
1 913889 . G A 372 PASS AA=G;AC=5;AF=0.625;AN=8;SPLICEAI=PERM1|0.00|0.01|0.00|0.00|-46|9|2|-45
1 914333 . C G 556 PASS AA=G;AC=5;AF=0.625;AN=8;SPLICEAI=PERM1|0.00|0.00|0.00|0.00|-3|27|-3|-38
1 914852 . G C 525 PASS AA=C;AC=5;AF=0.625;AN=8;SPLICEAI=PERM1|0.00|0.00|0.00|0.00|22|-22|48|49
1 914940 . T C 488 PASS AA=C;AC=5;AF=0.625;AN=8;SPLICEAI=PERM1|0.00|0.00|0.00|0.00|28|-30|-39|3
(...)