jvarkit
BreakdancerToVcf
Convert output of breakdancer to VCF
Usage
Usage: breakdancer2vcf [options] Files
Options:
--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
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --out
Output file. Optional . Default: stdout
--version
print version and exit
-R, -reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
Keywords
- cnv
- sv
- breakdancer
- vcf
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew breakdancer2vcf
The java jar file will be installed in the dist directory.
Creation Date
20200511
Source code
Unit Tests
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 breakdancer2vcf ? 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
input
Input is the tabular output of BreakDancer.
Genotypes are all set to 0/1.
Example:
$ wget -O - -q "https://raw.githubusercontent.com/genome/breakdancer/master/test-data/expected_output" | java -jar dist/breakdancer2vcf.jar -R src/test/resources/human_b37.dict
##fileformat=VCFv4.2
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Estimate allele Frequency">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=CHROM2,Number=1,Type=String,Description="Chromosome 2">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ORIENT1,Number=1,Type=String,Description="Orientation 1">
##INFO=<ID=ORIENT2,Number=1,Type=String,Description="Orientation 2">
##INFO=<ID=POS2,Number=1,Type=String,Description="Position 2">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Structural variation type">
##breakdancer.command=bdfast -o21 inv_del_bam_config
##breakdancer.version=1.4.1-unstable-10-fdfe9f2-dirty (commit fdfe9f2-dirty)
##breakdancer2vcf.meta=compilation:20200511120615 githash:c830e0b htsjdk:2.21.3 date:20200511120941 cmd:-R src/test/resources/human_b37.dict
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
(...)
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H_IJ-NA19238-NA19238-extlibs H_IJ-NA19240-NA19240-extlibs
21 29185056 . N <INS> 99 . DP=2;END=29185377;SVLEN=226;SVTYPE=INS GT:DP:GQ 0/1:1:99 0/1:1:99
21 29185462 . N <DEL> 99 . DP=21;END=29186122;SVLEN=-545;SVTYPE=DEL GT:AF:DP:GQ 0/1:176.58:21:99 0/1:167.89:.:99
21 34807694 . N <INS> 99 . DP=3;END=34808852;SVLEN=304;SVTYPE=INS GT:DP:GQ 0/1:1:99 0/1:2:99
21 34808937 . N <INV> 99 . DP=2;END=34809799;SVLEN=-737;SVTYPE=INV GT:AF:DP:GQ 0/1:847.39:.:99 0/1:878.83:2:99