jvarkit

VCFTrios

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Find mendelian incompatibilitie / denovo variants in a VCF

Usage

Usage: vcftrio [options] Files
  Options:
    -A, --attribute
      INFO Attribute name containing the name of the affected samples.
      Default: MENDEL
    -d, --dicard
      Discard the variant if there is NO mendelian violation.
      Default: false
    -fi, --filter-in
      FILTER name if there is ANY mendelian violation.
    -fo, --filter-out, --filter-no-denovo
      FILTER name if there is NO mendelian violation.
    -gtf, --gtfilter
      GENOTYPE FILTER name. Create a filter in the GENOTYPE column when there 
      is NO mendelian violation
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -hr, --hom-ref
      [20180705] treat NO_CALL genotypes as HOM_REF (when individual 
      VCF/Sample have been merged).
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -p, --ped, --pedigree
      Pedigree file. A pedigree is a text file delimited with tabs. No header. 
      Columns are (1) Family (2) Individual-ID (3) Father Id or '0' (4) Mother 
      Id or '0' (5) Sex : 1 male/2 female / 0 unknown (6) Status : 0 
      unaffected, 1 affected,-9 unknown
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcftrios/VCFTrios.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcftrios/VCFTriosTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcftrio ? 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

Using GATK VariantAnnotator ?

GATK VariantAnnotator doesn’t work if GQ is low or if there is no GQ.

Example

a pedigree file:

$  cat pedigree.txt 

A	SAMPLE_P	0	0	0
A	SAMPLE_M	0	0	0
A	SAMPLE_E	SAMPLE_P	SAMPLE_M	0

find mendelian incompatibilities:

$  gunzip -c input.vcf.gz |\
   java -jar dist/vcftrio.jar -p pedigree.txt | grep -E '(#CHROM|MENDEL=SAMPLE_E)' |\
   verticalize 

(...)
>>> 23
$1	#CHROM	X
$2	POS	0573
$3	ID	rs358
$4	REF	G
$5	ALT	A
$6	QUAL	85.60
$7	FILTER	PASS
$8	INFO	MENDEL=SAMPLE_E
$9	FORMAT	GT:DP:DP4:GP:GQ:PL
$10	SAMPLE_E	0/1:11:6,0,5,0:97,0,122:97:96,0,118
$11	SAMPLE_M	1/1:5:0,0,5,0:134,19,0:19:120,15,0
$12	SAMPLE_P	1/1:6:0,0,6,0:136,22,0:22:121,18,0
<<< 23
(...)
>>> 59
$1	#CHROM	Y
$2	POS	19
$3	ID	rs5678
$4	REF	CA
$5	ALT	C,CAA
$6	QUAL	31.86
$7	FILTER	PASS
$8	INFO	MENDEL=SAMPLE_E
$9	FORMAT	GT:DP:DP4:GP:GQ
$10	SAMPLE_E	2/2:80:3,0,43,34:.,.,108,.,203,0:99
$11	SAMPLE_M	.
$12	SAMPLE_P	1/1:53:0,0,27,26:81,99,0,.,.,.:81
<<< 59

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