jvarkit

VcfMoveFiltersToInfo

Move any FILTER to the INFO column. reset FILTER to PASS

Usage

Usage: java -jar dist/vcfmovefilterstoinfo.jar  [options] Files
Usage: vcfmovefilterstoinfo [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
    -f, --filter
      INFO name. This tag will be used to store the previous filters
      Default: PREVIOUSLY_FILTERED_AS
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -G, --genotype
      If not empty, FILTER all **GENOTYPES** with this filter, if any FILTER 
      was found. Could be useful before bcftools merge
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -t, --limitto
      If not empty, limit to those FILTERS. Multiple separated by comma/space.
      Default: []
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• vcf
• format
• info

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 vcfmovefilterstoinfo

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

Creation Date

20161025

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/burden/VcfMoveFiltersToInfo.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 vcfmovefilterstoinfo ? 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

For Matilde K: move the information in FILTER to the INFO column to keep a trace of the FILTERs.

Example

$ cat input.vcf | grep -v "##"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	16057607	rs201535778	G	GAAAA	.	.	AAC=2;AAF=0.0005;BEACON=T|solvebio,T|bob,T|solvebio-133,T|altruist,T|prism,T|kaviar;NS=3690;RAC=3688;RAF=0.9995;VTYPE=SNV
22	16057608	rs201535778	G	T	.	.	AAC=2;AAF=0.0005;BEACON=T|solvebio,T|bob,T|solvebio-133,T|altruist,T|prism,T|kaviar;NS=3690;RAC=3688;RAF=0.9995;VTYPE=SNV


$ java -jar dist/vcfmovefilterstoinfo.jar input.vcf | grep -v "##"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	16057608	rs201535778	G	T	.	.	AAC=2;AAF=0.0005;NS=3690;PREVIOUSLY_FILTERED_AS=FT1;RAC=3688;RAF=0.9995;VTYPE=SNV
22	16058492	.	G	A	.	.	AAC=2;AAF=0.0005;NS=3708;PREVIOUSLY_FILTERED_AS=FT2;RAC=3706;RAF=0.9995;VTYPE=SNV


$ java -jar dist/vcfmovefilterstoinfo.jar -f OLDFILTER -t FT2 input.vcf | grep -v "##"
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	16057608	rs201535778	G	T	.	FT1	AAC=2;AAF=0.0005;NS=3690;RAC=3688;RAF=0.9995;VTYPE=SNV
22	16058492	.	G	A	.	.	AAC=2;AAF=0.0005;NS=3708;OLDFILTER=FT2;RAC=3706;RAF=0.9995;VTYPE=SNV

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