FindAVariation

##Motivation

Reads a list of path to VCF files and find mutations (chrom-pos).

The program will try to fix the chromosome names according to the dictionary in the VCF headers.

##Compilation

See also Compilation.

$ make findamutation

##Synopsis

$ java -jar dist/findamutation.jar -p chr1:pos1  -p chr2:pos2  (stdin|list-of-path.txt) 

##Options

Option	Description
-p (chrom:pos)	Add a position to find. Can be called multiple times.
-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/misc/FindAMutation.java

##Example

$ find ./ -name "*.vcf" -o -name "*.vcf.gz" |\
   java -jar dist/findamutation.jar -p "chr1:1234" 

htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	1	8216713	8216713	yossi-1		NA12878	HET	A G
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	1	8216713	8216713	yossi-1		NA12891	HET	A G
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	1	8216713	8216713	yossi-1		NA12892	HET	A G
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	2	2	2	.		NA12878	HOM_REF	C C
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	2	2	2	.		NA12891	HET	C T
htsjdk/testdata/htsjdk/samtools/intervallist/IntervalListFromVCFTestManual.vcf	2	2	2	.		NA12892	HET	C T

##See also

• FindAllCoveragesAtPosition

##History

• 2014: Creation