ConvertBamChromosomes

Convert the names of the chromosomes in a BAM file

Usage

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

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

Usage: bamrenamechr [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --dict
      Use this new dictionary 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...)
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -i, --ignore
      If the tool cannot convert a contig, skip the read
      Default: false
    -f, --mapping, -m
      load a custom name mapping. Format (chrom-source\tchrom-dest\n)+
    -o, --out
      Output file. Optional . Default: stdout
    -R, --reference
      For Reading CRAM. Indexed fasta Reference file. This file must be 
      indexed with samtools faidx and with picard/gatk 
      CreateSequenceDictionary or samtools dict
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit

Keywords

• sam
• bam
• chromosome
• contig

See also in Biostars

• https://www.biostars.org/p/13462
• https://www.biostars.org/p/9479387

Creation Date

20131217

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/ConvertBamChromosomes.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/ConvertBamChromosomesTest.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 bamrenamechr ? 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

Example

$ cat samtools-0.1.19/examples/toy.sam

@SQ SN:ref  LN:45
@SQ SN:ref2 LN:40
r001    163 ref 7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG *   XX:B:S,12561,2,20,112
r002    0   ref 9   30  1S2I6M1P1I1P1I4M2I  *   0   0   AAAAGATAAGGGATAAA   *
r003    0   ref 9   30  5H6M    *   0   0   AGCTAA  *
r004    0   ref 16  30  6M14N1I5M   *   0   0   ATAGCTCTCAGC    *
r003    16  ref 29  30  6H5M    *   0   0   TAGGC   *
r001    83  ref 37  30  9M  =   7   -39 CAGCGCCAT   *
x1  0   ref2    1   30  20M *   0   0   aggttttataaaacaaataa    ????????????????????
x2  0   ref2    2   30  21M *   0   0   ggttttataaaacaaataatt   ?????????????????????
x3  0   ref2    6   30  9M4I13M *   0   0   ttataaaacAAATaattaagtctaca  ??????????????????????????
x4  0   ref2    10  30  25M *   0   0   CaaaTaattaagtctacagagcaac   ?????????????????????????
x5  0   ref2    12  30  24M *   0   0   aaTaattaagtctacagagcaact    ????????????????????????
x6  0   ref2    14  30  23M *   0   0   Taattaagtctacagagcaacta ???????????????????????

java -jar dist/bamrenamechr.jar \
   -f <(echo -e "ref\tCHROM1\nref2\tCHROM2")
   samtools-0.1.19/examples/toy.sam

@HD VN:1.4  SO:unsorted
@SQ SN:CHROM1   LN:45
@SQ SN:CHROM2   LN:40
@PG ID:0    PN:com.github.lindenb.jvarkit.tools.misc.ConvertBamChromosomes  VN:dfab75cb8c06e47e9989e59df62ec8f3242934c4 CL:-f /dev/fd/63 /commun/data/packages/samtools-0.1.19/examples/toy.sam
r001    163 CHROM1  7   30  8M4I4M1D3M  =   37  39  TTAGATAAAGAGGATACTG *   XX:B:S,12561,2,20,112
r002    0   CHROM1  9   30  1S2I6M1P1I1P1I4M2I  *   0   0   AAAAGATAAGGGATAAA   *
r003    0   CHROM1  9   30  5H6M    *   0   0   AGCTAA  *
r004    0   CHROM1  16  30  6M14N1I5M   *   0   0   ATAGCTCTCAGC    *
r003    16  CHROM1  29  30  6H5M    *   0   0   TAGGC   *
r001    83  CHROM1  37  30  9M  =   7   -39 CAGCGCCAT   *
x1  0   CHROM2  1   30  20M *   0   0   AGGTTTTATAAAACAAATAA    ????????????????????
x2  0   CHROM2  2   30  21M *   0   0   GGTTTTATAAAACAAATAATT   ?????????????????????
x3  0   CHROM2  6   30  9M4I13M *   0   0   TTATAAAACAAATAATTAAGTCTACA  ??????????????????????????
x4  0   CHROM2  10  30  25M *   0   0   CAAATAATTAAGTCTACAGAGCAAC   ?????????????????????????
x5  0   CHROM2  12  30  24M *   0   0   AATAATTAAGTCTACAGAGCAACT    ????????????????????????
x6  0   CHROM2  14  30  23M *   0   0   TAATTAAGTCTACAGAGCAACTA ???????????????????????

See also

• https://github.com/lindenb/jvarkit/blob/master/src/main/resources/chromnames/g1kv37_to_hg19.tsv
• https://github.com/lindenb/jvarkit/blob/master/src/main/resources/chromnames/hg19_to_g1kv37.tsv
• [[VcfRenameChromosomes]]
• http://plindenbaum.blogspot.fr/2013/07/g1kv37-vs-hg19.html

history

• 20180612 : rewrote it, using a output Dict, handle the SA tag