VcfBurdenCNV

Burden on CNV (experimental)

Usage

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

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

Usage: vcfburdencnv [options] Files
  Options:
    --cases
      File or comma-separated list of control samples
    --controls
      File or comma-separated list of control samples
    --default-overlap
      default fraction overlap for option --known
      Default: 0.75
    --exclude-bed
      BED regions to exclude
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --include-bed
      BED regions to include
    --jexl
      A Java EXpression Language (JEXL) expressions to filter the variants 
      from a VCF. Empty string will accept all variants. Expression returning 
      a TRUE will accept the variant. See 
      https://gatk.broadinstitute.org/hc/en-us/articles/360035891011 
    --known
      BED file containing the known frequent CNV. The 4th column must be a 
      number between 0 and 1, which well be the mutual overlap between the 
      known (e.g gnomad) variant and the user's variant. Default  value for 
      column 4 uses --default-overlap
    -o, --output
      Output file. Optional . Default: stdout
    --treshold
      do not display BED line if fisher > 'treshold'
      Default: 1.0E-5
    --version
      print version and exit

Keywords

• vcf
• burden
• cnv

Creation Date

20250404

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/burdencnv/VcfBurdenCNV.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 vcfburdencnv ? 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

Still in beta. Do not use.

INPUT

input is the set of vcf.gz indexed files or one file with the suffix '.list' containing the path to the vcfs

Example

wget -O - "https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/genome_sv/gnomad.v4.1.sv.sites.bed.gz" | gunzip -c |\
    awk -F '\t' '(NR>1 && $45="DEL" && $177>0.01 && $177!="NA") {L=int($3)-int($2);printf("%s\t%s\t%s\t%s\n",$1,$2,$3,(L>100?0.7:0.1));}' |\
    gzip > work/known.bed.gz


find MANTADIR -name "*.diploidSV.vcf.gz" > work/vcfs.list
java -jar jvarkit.jar vcfburdencnv \
    --cases work/cases.txt \
    --controls work/controls.txt \
    --known work/known.bed.gz \
    work/vcfs.list