jvarkit

VCFCombineTwoSnvs

Last commit

Detect Mutations than are the consequences of two distinct variants. This kind of variant might be ignored/skipped from classical variant consequence predictor. Idea from @SolenaLS and then @AntoineRimbert

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfcombinetwosnvs  [options] Files

Usage: vcfcombinetwosnvs [options] Files
  Options:
    -B, --bam
      Optional indexed BAM file used to get phasing information. This can be a 
      list of bam if the filename ends with '.list'
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    -P, --bedpe
      save optional report as bedpe
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
  * -g, --gtf
      A GTF (General Transfer Format) file. See 
      https://www.ensembl.org/info/website/upload/gff.html . Please note that 
      CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --maxRecordsInRam
      When writing  files that need to be sorted, this will specify the number 
      of records stored in RAM before spilling to disk. Increasing this number 
      reduces the number of file  handles needed to sort a file, and increases 
      the amount of RAM needed
      Default: 50000
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --version
      print version and exit

Keywords

vcf
annotation
prediction
protein
mnv

Creation Date

20160215

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfannot/VCFCombineTwoSnvs.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfannot/VCFCombineTwoSnvsTest.java

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.

Citing

Should you cite vcfcombinetwosnvs ? 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

Motivation

@SolenaLS ‘s idea: variant in the same codon give a new Amino acid undetected by annotaion tools.

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

KEYEXAMPLEDescription
CHROM1Chromosome for current variant.
REFCReference Allele for current variant
TRANSCRIPTuc001eik.3UCSC knownGene Transcript
cDdnaPos7+1 based position in cDNA
CodonPos7+1 based position of the codon in cNA
CodonWildGCCWild codon
AAPos3+1 based position of amino acid
AAWildAWild amino acid
POS1120612014+1 based position of variant 1
ID1.RS ID of variant 1
PosInCodon11Position in codon (1,2,3) of variant 1
Alt1AAlternate allele of variant 1
Codon1TCC Codon with variant 1 alone
AA1SAmino acid prediction for variant 1
INFO_*_11Data about alternate allele 1 taken out of original VCF
POS2120612013+1 based position of variant 1
ID2rs200646249RS ID of variant 1
PosInCodon22Position in codon (1,2,3) of variant 2
Alt2AAlternate allele of variant 2
Codon2GTC Codon with variant 2alone
AA2VAmino acid prediction for variant 2
INFO_*_21Data about alternate allele 2 taken out of original VCF
CombinedCodonTTCCombined codon with ALT1 and ALT2
CombinedAAFCombined amino acid with ALT1 and ALT2
CombinedSOnonsynonymous_variantSequence Ontology term
CombinedTypecombined_is_newtype of new mutation
N_READS_BOTH_VARIANTS168Number of reads carrying both variants
N_READS_NO_VARIANTS1045Number of reads carrying no variants
N_READS_TOTAL1213Total Number of reads
N_READS_ONLY_10Number of reads carrying onlt variant 1
N_READS_ONLY_20Number of reads carrying onlt variant 2