jvarkit

VcfBurdenMAF

Last commit

MAF for Cases / Controls

Usage

Usage: vcfburdenmaf [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
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -gtf, --gtf, --gtFiltered
      [20180117] Ignore FILTERed **Genotype**
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -c, -hr, --hr, --homref
      Treat No Call './.' genotypes as HOM_REF '0/0'
      Default: false
    -ignoreFiltered, --ignoreFiltered
      Don't try to calculate things why variants already FILTERed (faster)
      Default: false
    -M, --max-maf, --max-af
      select variants where MAF of cases OR MAF of control is lower or equal 
      than max-maf. A decimal number between 0.0 and 1.0. If the value ends 
      with '%' it is interpretted as a percentage eg. '1%' => '0.01'. A slash 
      '/' is interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 0.05
    -m, --min-maf, --min-af
      select variants where MAF of cases OR MAF of control is greater or 
      equals than min-maf. A decimal number between 0.0 and 1.0. If the value 
      ends with '%' it is interpretted as a percentage eg. '1%' => '0.01'. A 
      slash '/' is interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 0.0
    -o, --out
      Output file. Optional . Default: stdout
  * -p, --pedigree
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0:unknown;1:male;2:female), phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    -pfx, --prefix
      Prefix for FILTER/INFO. If it is empty and the variant is FILTERed, the 
      variant won'be written to output.
      Default: Burden
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfburdenmaf

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

Creation Date

20160418

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/burden/VcfBurdenMAF.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/burden/VcfBurdenMAFTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfburdenmaf ? 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

Variant in that VCF should have one and only one ALT allele. Use https://github.com/lindenb/jvarkit/wiki/VcfMultiToOneAllele if needed.

Output

Example

bcftools annotate -x 'INFO' src/test/resources/rotavirus_rf.ann.vcf.gz |\
	java -jar dist/vcfburdenmaf.jar --pedigree pedigree.ped

##fileformat=VCFv4.2
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##FILTER=<ID=BurdenMAFCas,Description="MAF of cases is greater than 0.05">
##FILTER=<ID=BurdenMAFCaseOrControls,Description="MAF of (cases OR controls) is greater than 0.05">
##FILTER=<ID=BurdenMAFControls,Description="MAF of controls is greater than 0.05">
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=BurdenMAFCas,Number=A,Type=Float,Description="Burden Filter F2. MAF Cases">
##INFO=<ID=BurdenMAFControls,Number=A,Type=Float,Description="Burden Filter F2. MAF Controls">
##contig=<ID=RF01,length=3302>
##contig=<ID=RF02,length=2687>
##contig=<ID=RF03,length=2592>
##contig=<ID=RF04,length=2362>
##contig=<ID=RF05,length=1579>
##contig=<ID=RF06,length=1356>
##contig=<ID=RF07,length=1074>
##contig=<ID=RF08,length=1059>
##contig=<ID=RF09,length=1062>
##contig=<ID=RF10,length=751>
##contig=<ID=RF11,length=666>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1	S2	S3	S4	S5
RF01	970	.	A	C	48.67	.	BurdenMAFCas=0.00;BurdenMAFControls=0.00	GT:PL	0/0:0,9,47	0/0:0,18,73	0/0:0,18,73	0/0:0,33,116	1/1:95,24,0
RF02	251	.	A	T	21.29	BurdenMAFCaseOrControls;BurdenMAFControls	BurdenMAFCas=0.00;BurdenMAFControls=0.500	GT:PL	0/0:0,15,57	0/1:31,0,5	0/1:31,0,5	0/0:0,9,42	0/0:0,24,69
RF02	578	.	G	A	53	.	BurdenMAFCas=0.00;BurdenMAFControls=0.00	GT:PL	0/0:0,33,122	0/0:0,39,135	0/0:0,39,135	1/1:100,30,0	0/0:0,27,109
RF02	877	.	T	A	3.45	BurdenMAFCas;BurdenMAFCaseOrControls	BurdenMAFCas=0.500;BurdenMAFControls=0.00	GT:PL	0/1:37,0,50	0/0:0,22,116	0/0:0,22,116	0/0:0,21,94	0/0:0,12,62
RF02	1726	.	T	G	8.23	BurdenMAFCaseOrControls;BurdenMAFControls	BurdenMAFCas=0.00;BurdenMAFControls=0.500	GT:PL	0/0:0,18,83	0/1:24,0,40	0/1:24,0,40	0/0:0,27,111	0/0:0,10,78
RF02	1962	.	TACA	TA	33.43	BurdenMAFCas;BurdenMAFCaseOrControls	BurdenMAFCas=0.500;BurdenMAFControls=0.00	GT:PL	0/1:70,0,159	0/0:0,15,225	0/0:0,15,225	0/0:0,27,231	0/0:0,27,168