jvarkit

MergeCnvNator

Last commit

Merge CNVNator results

Usage

Usage: mergecnvnator [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
    --bed
      limit to the calls overlaping that bed FILE
    --do-no-reuse
      Do not reuse a CNV if it was already used. Undocumented
      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].
    --hom-ref
      generate HOM_REF instead of NO_CALL for missing genotypes.
      Default: false
    --input-type
      Input type. Bed type is like cnvnator BUT the 4 first columns are 
      chrom,start,end,sample-name. 
      Default: cnvnator
      Possible Values: [cnvnator, bed]
    --max-cnv-size
      Skip CNVs having a length > 'x'. A distance specified as a positive 
      integer.Commas are removed. The following suffixes are interpreted : 
      b,bp,k,kb,m,mb 
      Default: 0
    --one-cnv-type
      Only one CNV type (del/dup) per variant.
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --ovr
      When counting the number of other CNVs overlapping the current CNV in 
      INFO/OV. Just report those having an overlap of at most 'x' with the 
      current variant. The idea is to ignore the big CNVs overlapping the 
      variant.A decimal number between 0.0 and 1.0. If the value ends with '%' 
      it is interpretted as a percentage eg. '1%' => '0.01'. A slash '/' is 
      interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 1.0
    -r, --ratio
      Two intervals are the same if they both have more or equals of this 
      fraction of length in common. A decimal number between 0.0 and 1.0. If 
      the value ends with '%' it is interpretted as a percentage eg. '1%' => 
      '0.01'. A slash '/' is interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 0.75
    --treshold
      Treshold between HET and HOM genotypes.A decimal number between 0.0 and 
      1.0. If the value ends with '%' it is interpretted as a percentage eg. 
      '1%' => '0.01'. A slash '/' is interpretted as a ratio. e.g: '1/100' => 
      '0.01'. 
      Default: 0.2
    --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
indel
cnvnator

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 mergecnvnator

The java jar file will be installed in the dist directory.

Creation Date

20181003

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/MergeCnvNator.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/MergeCnvNatorTest.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 mergecnvnator ? 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 CNVNator

(...)
deletion     chr2:1-2649000        2.649e+06  0        6.01633e-14  0            6.02087e-14  0           -1
duplication  chr2:3712001-3721000  9000       1.89036  0.0274362    5.17568e-42  0.137369     3.6838e-64  0.00821444
(...)

The name of each sample is the basename of the file, before the first .

a list of paths can be specified if the only input file ends with ‘.list’

Example

find DIR1 DIR2 -type f -name "*.tsv" > in.list
java -jar dist/mergecnvnator.jar -R ref.fasta in.list > out.vcf

(...)
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample7	Sample8	Sample9
chr1	1	.	N	<DEL>	.	.	END=10000;IMPRECISE;SVLEN=10000;SVTYPE=DEL	GT:CN:P1:P2:P3:P4:Q0:RD	1/1:0:1.594e-11:0.00:1.992e-11:0.00:-1.000e+00:0.00	1/1:0:1.594e-11:0.00:1.992e-11:0.00:-1.000e+00:0.00	1/1:0:1.594e-11:0.00:1.992e-11:0.00:-1.000e+00:0.00
chr1	40001	.	N	<DEL>	.	.	END=48000;IMPRECISE;SVLEN=8000;SVTYPE=DEL	GT:CN:P1:P2:P3:P4:Q0:RD	./.	./.	0/1:1:34.95:5.850e-06:323.37:2.143e-03:0.889:0.603
(...)

with bed files:

find . -type f -name "*.bed.gz" > jeter.list
java -jar ${JVARKIT_DIST}/mergecnvnator.jar --input-type bed 
-R ref.fasta jeter.list | bcftools sort -T . -O b -o 20201130.merge.bcf