Convert the names of the chromosomes in a Bed file
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar bedrenamechr [options] Files
Usage: bedrenamechr [options] Files
Options:
-c, --column
1-based chromosome column(s), multiple separated by commas
Default: 1
-convert, --convert
What should I do when a converstion is not found
Default: RAISE_EXCEPTION
Possible Values: [RAISE_EXCEPTION, SKIP, RETURN_ORIGINAL]
-d, --delim
field delimiter.
Default:
-s, --header
Ignore lines starting with this java regular expression
Default: (#|browser|track)
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
* -f, --mapping, -m, -R
load a custom name mapping.Chromosome mapping file. If the file looks
like a NGS file (fasta, vcf, bam...) the mapping is extracted from a
dictionary; Otherwise, it is interpreted as a mapping file ( See
https://github.com/dpryan79/ChromosomeMappings )
-o, --out
Output file. Optional . Default: stdout
--version
print version and exit
The project is licensed under the MIT license.
Should you cite bedrenamechr ? 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 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz |\
gunzip -c | \
java -jar dist/bedrenamechr.jar -f src/main/resources/chromnames/hg19_to_g1kv37.tsv -c 2 |\
tail
uc011nca.2 Y + 59213948 59276439 59230880 59274621 7 59213948,59222126,59230781,59233166,59252482,59272370,59274552, 59214117,59222281,59230919,59233257,59252550,59272463,59276439, P51809 uc011nca.2
uc004fxl.3 Y + 59213948 59276439 59222135 59274621 7 59213948,59222126,59230781,59233166,59252482,59272370,59274552, 59214117,59222216,59230919,59233257,59252550,59272463,59276439, P51809-3 uc004fxl.3
uc004fxk.3 Y + 59213948 59276439 59222135 59274809 7 59213948,59222126,59228291,59230781,59233166,59272370,59274552, 59214117,59222281,59228349,59230919,59233257,59272463,59276439, P51809-2 uc004fxk.3
uc011ncb.2 Y + 59213948 59276439 59222274 59274621 7 59213948,59222126,59230781,59233166,59252482,59272370,59274552, 59214117,59222277,59230919,59233257,59252550,59272463,59276439, B4DE96 uc011ncb.2
uc010nxr.2 Y + 59330251 59340490 59335611 59340461 9 59330251,59334000,59335576,59336119,59336347,59337090,59337948,59338753,59340193, 59330458,59334179,59335690,59336231,59336526,59337236,59338150,59338859,59340490, B4E011 uc010nxr.2
uc004fxm.1 Y + 59330251 59343488 59330414 59342523 9 59330251,59334078,59335552,59336119,59336354,59337119,59337948,59338753,59342486, 59330458,59334179,59335690,59336231,59336526,59337236,59338150,59338859,59343488, B9ZVT0 uc004fxm.1
uc004fxn.1 Y + 59330251 59343488 59330430 59343080 9 59330251,59335576,59336119,59336347,59337090,59337948,59338753,59340193,59342486, 59330458,59335690,59336231,59336526,59337236,59338150,59338859,59340278,59343488, Q01113 uc004fxn.1
uc004fxo.1 Y + 59352972 59356131 59353631 59356130 7 59352972,59354351,59354669,59354993,59355369,59355682,59355972, 59353819,59354463,59354816,59355130,59355505,59355884,59356131, I3L0A4 uc004fxo.1
uc022cpg.1 Y + 59354984 59358336 59355427 59358045 7 59354984,59355369,59355682,59355972,59356790,59357702,59357911, 59355130,59355505,59355884,59356131,59356943,59357771,59358336, Q9NQA3 uc022cpg.1
uc011ncc.1 Y - 59358328 59360854 59358328 59358328 3 59358328,59360006,59360500, 59359508,59360115,59360854, uc011ncc.1