jvarkit
IndexCovToVcf
convert indexcov data to vcf
Usage
Usage: indexcov2vcf [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, --output
Output file. Optional . Default: stdout
-p, --pedigree
Optional Pedigree. A pedigree file. tab delimited. Columns:
family,id,father,mother, sex:(0:unknown;1:male;2:female), phenotype
(-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected)
-R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
-t, --treshold
DUP if 1.5-x<=depth<=1.5+x . HET_DEL if 0.5-x<=depth<=0.5+x HOM_DEL if
0.0-x<=depth<=0.0+x.. 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: 0.05
--version
print version and exit
Keywords
- cnv
- duplication
- deletion
- sv
- indexcov
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 indexcov2vcf
The java jar file will be installed in the dist directory.
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 indexcov2vcf ? 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 a tab-delimited file created by e.g: indexcov (https://github.com/brentp/goleft/tree/master/indexcov)
#chrom start end SampleBB SampleBC SampleBD SampleBE SampleBF SampleBG SampleBH
chr1 23778 40778 1.59 1.31 1.67 1.61 1.83 1.52 1.48
chr1 29106 46106 1.9 1.54 1.72 1.97 1.88 1.53 1.95
chr1 84581 101581 0.764 0.841 1.2 1.16 1.18 1.13 1.23
chr1 15220 32220 0.355 0.704 1.09 0.784 0.81 1.37 0.954
chr1 58553 75553 0.353 0.436 0.912 0.836 1.16 1.09 0.611
chr1 19347 36347 0.381 0.411 0.811 0.795 1.16 1.22 0.495
chr1 81062 98062 1.09 0.972 1.35 1.22 1.66 1.76 1.1
chr1 17353 34353 1.06 1.06 1.23 1.26 1.44 1.43 1.03
chr1 48498 65498 1.08 0.996 1.28 1.44 1.52 1.57 1.05
output:
##fileformat=VCFv4.2
##FILTER=<ID=ALL_DEL,Description="number of samples >1 and all are deletions">
##FILTER=<ID=ALL_DUP,Description="number of samples >1 and all are duplication">
##FILTER=<ID=NO_SV,Description="There is no DUP or DEL in this variant">
##FORMAT=<ID=DEL,Number=1,Type=Integer,Description="set to 1 if relative number of copy <= 0.6">
##FORMAT=<ID=DUP,Number=1,Type=Integer,Description="set to 1 if relative number of copy >= 1.9">
##FORMAT=<ID=F,Number=1,Type=Float,Description="Relative number of copy: 0.5 deletion 1 normal 2.0 duplication">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=NDEL,Number=1,Type=Integer,Description="Number of samples being deleted">
##INFO=<ID=NDUP,Number=1,Type=Integer,Description="Number of samples being duplicated">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleBB SampleBC SampleBD SampleBE SampleBF (...)
chr1 0 . N <DUP> . . END=16384;NDEL=0;NDUP=8 GT:DUP:F 0:0:1.59 0:0:1.31 0:0:1.67 0:0:1.61 0:0:1.83 (...)
history
- 20191112 : add pedigree