Biostar9556602

Filtering of tricky overlapping sites in VCF

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar9556602  [options] Files

Usage: biostar9556602 [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
    -filter, --filter
      if not blank, do not remove the variants but set the FILTER with this 
      value 
    --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
    -sorter, --sorter
      Best variant sort type
      Default: LOWEST_AF
      Possible Values: [LOWEST_AF, HIGHEST_AF, LOWEST_DP, HIGHEST_DP, LOWEST_QUAL, HIGHEST_QUAL]
    --version
      print version and exit

Keywords

• vcf
• filter

See also in Biostars

• https://www.biostars.org/p/9556602

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar9556602.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 biostar9556602 ? 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

input

input must be sorted on coordinate, Alleles must be normalized (one ALT per variant)

Example

$ grep -v "##" jeter.vcf
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   905593  .   A   T   3887.15 PASS    AF=0.1
1   905594  rs867360694 A   T   3887.15 PASS    AF=0.1
1   905594  rs867360694 A   TT  3887.15 PASS    AF=0.2
1   905594  rs867360694 A   TTT 3887.15 PASS    AF=0.3
1   905595  .   A   T   3887.15 PASS    AF=0.1
1   905595  .   A   G   3887.15 PASS    AF=0.01


$ java -jar dist/jvarkit.jar biostar9556602 --sorter HIGHEST_AF  jeter.vcf --filter ZZZZZZZZZZZZ | grep -v "##"
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   905593  .   A   T   3887.15 PASS    AF=0.1
1   905594  rs867360694 A   TTT 3887.15 PASS    AF=0.3
1   905594  rs867360694 A   TT  3887.15 ZZZZZZZZZZZZ    AF=0.2
1   905594  rs867360694 A   T   3887.15 ZZZZZZZZZZZZ    AF=0.1
1   905595  .   A   T   3887.15 PASS    AF=0.1
1   905595  .   A   G   3887.15 ZZZZZZZZZZZZ    AF=0.01

$ java -jar dist/jvarkit.jar biostar9556602 --sorter LOWEST_AF  jeter.vcf  | grep -v "##"#CHROM POS ID  REF ALT QUAL    FILTER  INFO
1   905593  .   A   T   3887.15 PASS    AF=0.1
1   905594  rs867360694 A   T   3887.15 PASS    AF=0.1
1   905595  .   A   G   3887.15 PASS    AF=0.01