VcfLiftOver
Lift-over a VCF file
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcfliftover [options] Files
Usage: vcfliftover [options] Files
Options:
--adaptivematch
Use adapative liftover minmatch using the ratio between the min allele
size and the longest allele size
Default: false
--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
* -f, --chain
LiftOver chain file. Can be a local chain file, a URL 'https://hgdownload.soe.ucsc.edu/goldenpath/hg19/liftOver/hg19ToCriGri1.over.chain.gz',
or a chain identifier like 'hg19ToHg38'.
-check, --check
Check variant allele sequence is the same on REF
Default: false
-x, --failed
(file.vcf) write variants failing the liftOver here. Optional.
-failtag, --failtag
failed INFO tag
Default: LIFTOVER_FAILED
--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].
--ignore-chain-validation
Ignore LiftOver chain validation
Default: false
--indel, --indels
do not LiftOver indels
Default: false
--info
remove attribute from INFO on the fly
Default: []
-m, --minmatch
lift over min-match.
Default: 0.95
-o, --out
Output file. Optional . Default: stdout
* -D, -R, -r, --reference
Destination Reference. Indexed fasta Reference file. This file must be
indexed with samtools faidx and with picard/gatk
CreateSequenceDictionary or samtools dict
-T, --tag
INFO tag
Default: LIFTOVER
--version
print version and exit
Keywords
- vcf
- liftover
Creation Date
20240114
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 vcfliftover ? 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
Warning
you'd better have a look at gatk/picard LiftOverVcf
Example
Lift over a hg19 file to hg18
Before liftover:
$ curl -s "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" | grep -v "#
chr1 145273345 . T C 289.85 . . GT:AD:DP:GQ:PL 0/0:226,22:250:99:0,158,4259 0/1:224,24:250:5.77:6,0,5314 0/1:219,28:249:57.30:57,0,5027 0/1:215,34:250:99:269,0,3796
chr1 156011444 . T C 2523.46 . . GT:AD:DP:GQ:PL 0/1:24,15:40:99:214,0,443 0/1:32,36:68:99:702,0,794 1/1:1,59:61:99:1656,132,0 0/0:34,1:35:69.10:0,69,717
chr5 64982321 . T C 61.12 . . GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 1/1:0,1:1:3.01:37,3,0 ./. ./.
chr10 1142208 . T C 3404.30 . . GT:AD:DP:GQ:PL 1/1:1,37:39:87.16:940,87,0 1/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 1/1:0,30:30:75.18:836,75,0
chr10 126678092 . G A 89.08 . . GT:AD:DP:GQ:PL 0/0:64,3:67:99:0,165,1505 0/0:11,1:12:7.31:0,7,240 0/0:52,10:62:54.97:0,55,1263 0/1:35,9:44:99:125,0,693
chr10 135210791 . T C 65.41 . . GT:AD:DP:GQ:PL 0/0:4,0:4:9:0,9,84 1/1:0,3:3:6.02:74,6,0 1/1:0,1:1:3.01:37,3,0 0/0:3,0:3:9.02:0,9,100
chr13 48873835 . G A 58.95 . . GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6.01:62,6,0 1/1:0,1:1:3.01:31,3,0
chr20 36779424 . G A 128.76 . . GT:AD:DP:GQ:PL 0/0:49,1:52:63.68:0,64,969 0/0:17,0:17:30.05:0,30,320 0/0:93,0:94:99:0,216,2384 0/1:24,9:33:99:165,0,505
chrX 17819377 . T C 7515.25 . . GT:AD:DP:GQ:PL 1/1:0,125:126:99:2343,237,0 1/1:0,26:26:78.14:837,78,0 1/1:0,90:92:99:2640,244,0 1/1:0,74:75:99:1695,171,0
Running the liftover:
$ curl -s "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" |\
java -jar dist/jvarkit.jar vcfliftover \
-f hg19ToHg18 \
-X failing.vcf |\
grep -v "#"
chr1 143984702 . T C 289.85 . LIFTOVER=chr1|145273345 GT:AD:DP:GQ:PL0/0:226,22:250:99:0,158,4259 0/1:224,24:250:5.77:6,0,5314 0/1:219,28:249:57.30:57,0,5027 0/1:215,34:250:99:269,0,3796
chr1 154278068 . T C 2523.46 . LIFTOVER=chr1|156011444 GT:AD:DP:GQ:PL0/1:24,15:40:99:214,0,443 0/1:32,36:68:99:702,0,794 1/1:1,59:61:99:1656,132,0 0/0:34,1:35:69.10:0,69,717
chr5 65018077 . T C 61.12 . LIFTOVER=chr5|64982321 GT:AD:DP:GQ:PL1/1:0,2:2:6:58,6,0 1/1:0,1:1:3.01:37,3,0 ./. ./.
chr10 1132208 . T C 3404.30 . LIFTOVER=chr10|1142208 GT:AD:DP:GQ:PL 1/1:1,37:39:87.16:940,87,0 1/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 1/1:0,30:30:75.18:836,75,0
chr10 126668082 . G A 89.08 . LIFTOVER=chr10|126678092 GT:AD:DP:GQ:PL 0/0:64,3:67:99:0,165,1505 0/0:11,1:12:7.31:0,7,240 0/0:52,10:62:54.97:0,55,1263 0/1:35,9:44:99:125,0,693
chr10 135060781 . T C 65.41 . LIFTOVER=chr10|135210791 GT:AD:DP:GQ:PL 0/0:4,0:4:9:0,9,84 1/1:0,3:3:6.02:74,6,0 1/1:0,1:1:3.01:37,3,0 0/0:3,0:3:9.02:0,9,100
chr13 47771836 . G A 58.95 . LIFTOVER=chr13|48873835 GT:AD:DP:GQ:PL./. ./. 1/1:0,2:2:6.01:62,6,0 1/1:0,1:1:3.01:31,3,0
chr20 36212838 . G A 128.76 . LIFTOVER=chr20|36779424 GT:AD:DP:GQ:PL0/0:49,1:52:63.68:0,64,969 0/0:17,0:17:30.05:0,30,320 0/0:93,0:94:99:0,216,2384 0/1:24,9:33:99:165,0,505
chrX 17729298 . T C 7515.25 . LIFTOVER=chrX|17819377 GT:AD:DP:GQ:PL1/1:0,125:126:99:2343,237,0 1/1:0,26:26:78.14:837,78,0 1/1:0,90:92:99:2640,244,0 1/1:0,74:75:99:1695,171,0