jvarkit

VcfRenameSamples

Rename the Samples in a VCF

Usage

Usage: vcfrenamesamples [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --outputbcf
      Output bcf (for streams)
      Default: false
    --vcfcreateindex
      VCF, create tribble or tabix Index when writing a VCF/BCF to a file.
      Default: false
    --vcfmd5
      VCF, create MD5 checksum when writing a VCF/BCF to a file.
      Default: false
    --version
      print version and exit
    -E
      error like src sample missing in VCF
      Default: false
  * -f
      Tab delimited file containing old-name\tnew-name

Keywords

• vcf
• sample

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 vcfrenamesamples

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfRenameSamples.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 vcfrenamesamples ? 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

$ curl -s "https://raw.github.com/arq5x/gemini/master/test/test1.snpeff.vcf" |\
grep -A 2 CHROM  | cut -f 1-5,10-

#CHROM	POS	ID	REF	ALT	1094PC0005	1094PC0009	1094PC0012	1094PC0013
chr1	30860	.	G	C	0/0:7,0:7:15.04:0,15,177	0/0:2,0:2:3.01:0,3,39	0/0:6,0:6:12.02:0,12,143	0/0:4,0:4:9.03:0,9,119
chr1	69270	.	A	G	./.	./.	1/1:0,3:3:9.03:106,9,0	1/1:0,6:6:18.05:203,18,0

curl -s "https://raw.github.com/arq5x/gemini/master/test/test1.snpeff.vcf" |\
java -jar dist/vcfrenamesamples.jar -f <(echo -e "1094PC0005\tALPHA\n1094PC0012\tBETA\nSAMPLE\tGAMMA\n1094PC0009\tEPSILON") -E  |\
grep -A 2 "#CHROM" | cut -f 1-5,10-

#CHROM	POS	ID	REF	ALT	ALPHA	EPSILON	BETA	1094PC0013
chr1	30860	.	G	C	0/0:7,0:7:15:0,15,177	0/0:2,0:2:3:0,3,39	0/0:6,0:6:12:0,12,143	0/0:4,0:4:9:0,9,119
chr1	69270	.	A	G	./.	./.	1/1:0,3:3:9:106,9,0	1/1:0,6:6:18:203,18,0

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