jvarkit

IjgvdToVcf

Convert zips of Integrative Japanese Genome Variation to VCF file.

DEPRECATED

Deprecated since data are now available as VCF

Usage

Usage: ijgv2vcf [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].
    -F, --no-filtered
      ignore 'filtered' entries
      Default: false
    -M, --no-multiallelic
      ignore 'multiallelic' entries
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --version
      print version and exit

Keywords

• vcf
• jgvd
• japan
• tommo

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 ijgv2vcf

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

Creation Date

20190717

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/ijgvd/IjgvdToVcf.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 ijgv2vcf ? 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

DEPRECATED

Deprecated since data are now available as VCF

DESCRIPTION

Integrative Japanese Genome Variation (iJGVD https://ijgvd.megabank.tohoku.ac.jp/ ) provides data of genomic variations obtained by whole-genome sequencing of Japanese individuals, who participate in the genome cohort study by ToMMo, IMM and other cohort projects in Japan.

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals, Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabat a Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegi shi N, Douglas Engel J, Kinoshita K, Kure S, Yaegashi N, ToMMo Japanese Reference Panel Project and Yamamoto M, Nat Commun, 21; 6:8018 (2015)

##Example

$ ls ~/Downloads/chr* ~/Downloads/multiallelic_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip 
~/Downloads/chr10_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr11_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr1_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr12_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr13_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr14_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr15_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr16_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr17_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr18_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr19_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr20_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr21_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr2_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr22_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr3_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr4_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr5_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr6_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr7_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr8_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/chr9_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip
~/Downloads/multiallelic_20190717170045-bd410447a29ca7b9eb95ed92bf11b473.zip


$ java -jar dist/ijgv2vcf.jar -R ~/src/jvarkit-git/src/test/resources/human_b37.dict ~/Downloads/*.zip > out.vcf

$ java -jar dist/ijgv2vcf.jar -F -M -R ~/src/jvarkit-git/src/test/resources/human_b37.dict ~/Downloads/*.zip | bcftools view -O z -o ~/Downloads/3.5KJPN_tommo_2019071.vcf.gz
$ ls -lah ~/Downloads/3.5KJPN_tommo_2019071.vcf.gz
-rw-r--r-- 1 lindenb lindenb 514M juil. 17 15:04 ~/Downloads/3.5KJPN_tommo_2019071.vcf.gz

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