VCFCombineTwoSnvs

##Motivation

Idea from @SolenaLS and then @AntoineRimbert

##Compilation

See also Compilation.

$  make vcfcombinetwosnvs

##Synopsis

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

Options

• -k KnownGene data URI/File. Beware chromosome names are formatted the same as your REFERENCE. * -B Optional indexed BAM file used to get phasing information. * -o,--output output file.
• -h,--help print help
• -version,--version show version and exit

##Source Code

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

Output

Example

##fileformat=VCFv4.2
##FILTER=<ID=TwoStrands,Description="(number of reads carrying both mutation) < (reads carrying variant 1 + reads carrying variant 2)">
##INFO=<ID=CodonVariant,Number=.,Type=String,Description="Variant affected by two distinct mutation. Format is defined in the INFO column. INFO_AC:Allele count in genotypes, for each ALT allele, in the same order as listed.INFO_AF:Allele Frequency, for each ALT allele, in the same order as listed.INFO_MLEAC:Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed.INFO_MLEAF:Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed.">
##VCFCombineTwoSnvsCmdLine=-k jeter.knownGene.txt -tmpdir tmp/ -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37.fasta -B /commun/data/projects/plateforme/NTS-017_HAL_Schott_mitral/20141106/align20141106/Samples/CD13314/BAM/Haloplex20141106_CD13314_final.bam
##VCFCombineTwoSnvsHtsJdkHome=/commun/data/packages/htsjdk/htsjdk-2.0.1
##VCFCombineTwoSnvsHtsJdkVersion=2.0.1
##VCFCombineTwoSnvsVersion=c5af7d1bd367562b3578d427d24ec62856835d38
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	120612013	rs200646249	G	A	.	.	CodonVariant=CHROM|1|REF|G|TRANSCRIPT|uc001eil.3|cDdnaPos|8|CodonPos|7|CodonWild|GCC|AAPos|3|AAWild|A|POS1|120612013|ID1|rs200646249|PosInCodon1|2|Alt1|A|Codon1|GTC|AA1|V|INFO_MLEAC_1|1|INFO_AC_1|1|INFO_MLEAF_1|0.500|INFO_AF_1|0.500|POS2|120612014|ID2|.|PosInCodon2|1|Alt2|A|Codon2|TCC|AA2|S|INFO_MLEAC_2|1|INFO_AC_2|1|INFO_MLEAF_2|0.500|INFO_AF_2|0.500|CombinedCodon|TTC|CombinedAA|F|CombinedSO|nonsynonymous_variant|CombinedType|combined_is_new|N_READS_BOTH_VARIANTS|168|N_READS_NO_VARIANTS|1045|N_READS_TOTAL|1213|N_READS_ONLY_1|0|N_READS_ONLY_2|0,CHROM|1|REF|G|TRANSCRIPT|uc001eik.3|cDdnaPos|8|CodonPos|7|CodonWild|GCC|AAPos|3|AAWild|A|POS1|120612013|ID1|rs200646249|PosInCodon1|2|Alt1|A|Codon1|GTC|AA1|V|INFO_MLEAC_1|1|INFO_AC_1|1|INFO_MLEAF_1|0.500|INFO_AF_1|0.500|POS2|120612014|ID2|.|PosInCodon2|1|Alt2|A|Codon2|TCC|AA2|S|INFO_MLEAC_2|1|INFO_AC_2|1|INFO_MLEAF_2|0.500|INFO_AF_2|0.500|CombinedCodon|TTC|CombinedAA|F|CombinedSO|nonsynonymous_variant|CombinedType|combined_is_new|N_READS_BOTH_VARIANTS|168|N_READS_NO_VARIANTS|1045|N_READS_TOTAL|1213|N_READS_ONLY_1|0|N_READS_ONLY_2|0;EXAC03_AC_NFE=641;EXAC03_AN_NFE=48948
1	120612014	.	C	A	.	.	CodonVariant=CHROM|1|REF|C|TRANSCRIPT|uc001eik.3|cDdnaPos|7|CodonPos|7|CodonWild|GCC|AAPos|3|AAWild|A|POS1|120612014|ID1|.|PosInCodon1|1|Alt1|A|Codon1|TCC|AA1|S|INFO_MLEAC_1|1|INFO_AC_1|1|INFO_MLEAF_1|0.500|INFO_AF_1|0.500|POS2|120612013|ID2|rs200646249|PosInCodon2|2|Alt2|A|Codon2|GTC|AA2|V|INFO_MLEAC_2|1|INFO_AC_2|1|INFO_MLEAF_2|0.500|INFO_AF_2|0.500|CombinedCodon|TTC|CombinedAA|F|CombinedSO|nonsynonymous_variant|CombinedType|combined_is_new|N_READS_BOTH_VARIANTS|168|N_READS_NO_VARIANTS|1045|N_READS_TOTAL|1213|N_READS_ONLY_1|0|N_READS_ONLY_2|0,CHROM|1|REF|C|TRANSCRIPT|uc001eil.3|cDdnaPos|7|CodonPos|7|CodonWild|GCC|AAPos|3|AAWild|A|POS1|120612014|ID1|.|PosInCodon1|1|Alt1|A|Codon1|TCC|AA1|S|INFO_MLEAC_1|1|INFO_AC_1|1|INFO_MLEAF_1|0.500|INFO_AF_1|0.500|POS2|120612013|ID2|rs200646249|PosInCodon2|2|Alt2|A|Codon2|GTC|AA2|V|INFO_MLEAC_2|1|INFO_AC_2|1|INFO_MLEAF_2|0.500|INFO_AF_2|0.500|CombinedCodon|TTC|CombinedAA|F|CombinedSO|nonsynonymous_variant|CombinedType|combined_is_new|N_READS_BOTH_VARIANTS|168|N_READS_NO_VARIANTS|1045|N_READS_TOTAL|1213|N_READS_ONLY_1|0|N_READS_ONLY_2|0;EXAC03_AC_NFE=640;EXAC03_AN_NFE=48228

Fields

KEY	EXAMPLE	DESC
CHROM	1	Chromosome for current variant.
REF	C	Reference Allele for current variant
TRANSCRIPT	uc001eik.3	UCSC knownGene Transcript
cDdnaPos	7	+1 based position in cDNA
CodonPos	7	+1 based position of the codon in cNA
CodonWild	GCC	Wild codon
AAPos	3	+1 based position of amino acid
AAWild	A	Wild amino acid
POS1	120612014	+1 based position of variant 1
ID1	.	RS ID of variant 1
PosInCodon1	1	Position in codon (1,2,3) of variant 1
Alt1	A	Alternate allele of variant 1
Codon1	TCC	Codon with variant 1 alone
AA1	S	Amino acid prediction for variant 1
INFO_*_1	1	Data about alternate allele 1 taken out of original VCF
POS2	120612013	+1 based position of variant 2
ID2	rs200646249	RS ID of variant 2
PosInCodon2	2	Position in codon (1,2,3) of variant 2
Alt2	A	Alternate allele of variant 2
Codon2	GTC	Codon with variant 2 alone
AA2	V	Amino acid prediction for variant 2
INFO_*_2	1	Data about alternate allele 2 taken out of original VCF
CombinedCodon	TTC	Combined codon with ALT1 and ALT2
CombinedAA	F	Combined amino acid with ALT1 and ALT2
CombinedSO	nonsynonymous_variant	Sequence Ontology term
CombinedType	combined_is_new	type of new mutation
N_READS_BOTH_VARIANTS	168	Number of reads carrying both variants
N_READS_NO_VARIANTS	1045	Number of reads carrying no variants
N_READS_TOTAL	1213	Total Number of reads
N_READS_ONLY_1	0	Number of reads only carrying variant 1
N_READS_ONLY_2	0	Number of reads only carrying variant 2

Contribute

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

##History

• 2016 : Creation

License

The project is licensed under the MIT license.