jvarkit

VcfSamplesPRS

another program for @AntoineRimbert

Usage

Usage: java -jar dist/vcfsamplesprs.jar  [options] Files
Usage: vcfsamplesprs [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
  * --score, --scores, -S
      tabix indexed scores. 
      CHROM(tab)POS(tab)ID(tab)REF(tab)ALT(tab)EFFECT_ALL(tab)EFFECT 
    --version
      print version and exit

Keywords

• vcf
• indel

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 vcfsamplesprs

The java jar file will be installed in the dist directory.

Creation Date

20220915

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/prs/VcfSamplesPRS.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 vcfsamplesprs ? 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

buid tabix database

$ head AR_test.txt | column -t
#CHROM  POS        ID          REF  ALT  EFFECT_ALL  EFFECT  
chr1    5550460   rs249409   G    A    G           0.052
chr1    10918306  rs69301    G    T    T           0.15
chr2    2126390   rs13617   G    A    A           0.1
chr2    4407256   rs476   G    T    G           0.071
chr6    1605860  rs1564348   T    C    T           0.014
chr6    2093141   rs18   G    A    G           0.057

LC_ALL=C sort -T . -t $'\t' -k1,1 -k2,2n  AR_test.txt | bgzip > AR_test.txt.gz
tabix -s1 -b 2 -e 2  -c '#' 20220915_AR_test.txt.gz

and then

bcftools view in.bcf | java -jar dist/vcfsamplesprs.jar -S AR_test.txt.gz

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