VCFTrio

##Motivation Check for mendelian incompatibilities in a VCF.

##Synopsis

$ java -jar dist/vcftrio.jar [options] (stdin|file.vcf) 

###Compilation

See also Compilation.

$ make vcftrio

##Options

Option	Description
-p (file)	Pedigree file (Family/name/father/mother/sex)
-f	create a filter in the FILTER column
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.
--doap	prints a DOAP+XML description of the program and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/vcftrios/VCFTrios.java

##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

##History

• 2014: Creation

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.