jvarkit

BamLiftOver

Lift-over a BAM file.

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar bamliftover  [options] Files

Usage: bamliftover [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
  * -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'.
  * -R2, --destination-dict
      A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
    --drop-seq
      drop SEQ and QUAL
      Default: false
    -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
    -o, --out
      Output file. Optional . Default: stdout
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --regions
      Limit analysis to this interval. A source of intervals. The following 
      suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz, 
      gtf.gz.Otherwise it could be an empty string (no interval) or a list of 
      plain interval separated by '[ \t\n;,]'
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --save-position
      Save original position in SMA attribute
      Default: false
    --unmapped
      discard unmapped reads/unlifted reads
      Default: false
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit

Keywords

• bam
• liftover

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/BamLiftOver.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 bamliftover ? 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

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