LiftOver a BED file
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar bedliftover [options] Files
Usage: bedliftover [options] Files
Options:
* -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'.
-c, --columns
column indexes for chrom,start,end. Multiple chrom/start/end can be set
by groups of 3 intergers: e.g '1,2,3,6,7,8,10,11,12'
Default: 1,2,3
--chainvalid, --disable-chain-validation
Ignore LiftOver chain validation
Default: false
-x, --failed
write bed failing the liftOver here. Optional.
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-m, --minmatch
lift over min-match.
Default: 0.95
--original, --src
Append original interval as CHROM:START-END
Default: false
-o, --output
Output file. Optional . Default: stdout
* -D, -R2, -R, -r, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard/gatk CreateSequenceDictionary or samtools dict
--version
print version and exit
-1
coordinates are one-based (input is NOT bed)
Default: false
-R1
Source of chromosome names to convert chromosome names ('chr1'->'1') for
the source assembly. Could be a dict, a fai, etc...
20140311
The project is licensed under the MIT license.
Should you cite bedliftover ? 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
cat in.bed | java -jar jvarkit.jar bedliftover --chain x.chain -R ref.fa