VcfSpliceAI

Annotate VCF with local spiceai vcf

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:
  * --vcf, --annotation, --spliceai
      SpliceAI VCF.vcf.gz indexed with tabix
    --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
    --buffer
      When we're looking for variants in a lare VCF file, load the variants in 
      an interval of 'N' bases instead of doing a random access for each 
      variant. 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
    --tag
      INFO tag
      Default: SpliceAI
    --version
      print version and exit

Keywords

• vcf
• splice
• splicing
• spliceai

Creation Date

20201107

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/spliceai/VcfSpliceAI.java

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 --annot /path/to/spliceai_scores.masked.indel.hg38.vcf.gz  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
(...)