VcfCompareCallers

##Motivation

Compare two VCFs and print common/exclusive information for each sample/genotype

##Compilation

See also Compilation.

$  make vcfcomparecallers

##Synopsis

$ java -jar dist/vcfcomparecallers.jar.jar file1.vcf(.gz) stdin 
$ java -jar dist/vcfcomparecallers.jar.jar file1.vcf(.gz) file2.vcf(.gz) 

##Options

Option	Description
-o (filename)	output file. default:stdout
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

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

##Example

$ java -jar dist-1.128/vcfcomparecallers.jar  Proj1.samtools.vcf.gz  Proj1.varscan.vcf.gz
#Sample	unique_to_file_1	unique_to_file_1_snp	unique_to_file_1_indel	unique_to_file_2	unique_to_file_2_snp	unique_to_file_2_indel	common	common_snp	common_indel	called_and_same	called_but_discordant
NA12892	5	4	1	1	0	1	14	14	0	14	0
NA12891	4	3	1	1	0	1	13	13	0	13	0
NA12878	3	2	1	1	0	1	13	13	0	13	0

$ java -jar dist-1.128/vcfcomparecallers.jar  Proj1.samtools.vcf.gz  Proj1.varscan.vcf.gz | verticalize

>>> 2
$1                  #Sample : NA12892
$2         unique_to_file_1 : 5
$3     unique_to_file_1_snp : 4
$4   unique_to_file_1_indel : 1
$5         unique_to_file_2 : 1
$6     unique_to_file_2_snp : 0
$7   unique_to_file_2_indel : 1
$8                   common : 14
$9               common_snp : 14
$10            common_indel : 0
$11         called_and_same : 14
$12   called_but_discordant : 0
<<< 2

>>> 3
$1                  #Sample : NA12891
$2         unique_to_file_1 : 4
$3     unique_to_file_1_snp : 3
$4   unique_to_file_1_indel : 1
$5         unique_to_file_2 : 1
$6     unique_to_file_2_snp : 0
$7   unique_to_file_2_indel : 1
$8                   common : 13
$9               common_snp : 13
$10            common_indel : 0
$11         called_and_same : 13
$12   called_but_discordant : 0
<<< 3

>>> 4
$1                  #Sample : NA12878
$2         unique_to_file_1 : 3
$3     unique_to_file_1_snp : 2
$4   unique_to_file_1_indel : 1
$5         unique_to_file_2 : 1
$6     unique_to_file_2_snp : 0
$7   unique_to_file_2_indel : 1
$8                   common : 13
$9               common_snp : 13
$10            common_indel : 0
$11         called_and_same : 13
$12   called_but_discordant : 0
<<< 4

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues`
• Source Code: http://github.com/lindenb/jvarkit

##See also

##History

• 2015 : Creation

License

The project is licensed under the MIT license.