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BamRenameChromosomes
Pierre Lindenbaum edited this page Dec 17, 2013
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##Motivation
Rename chromosomes in a BAM file (eg. convert hg19/ucsc to grch37/ensembl).
##Compilation
See also Compilation.
$ ant bamrenamechr
##Usage
$ java -jar dist/bamrenamechr.jar -f mapping.tsv -C (stdin|in.bam|in.sam) > out.sam
##Options
Option | Description |
---|---|
-o (filename.bam) | Filename output. optional (default: SAM to stdout) |
-f (file.tsv) | Mapping file. Format (chrom-source\tchrom-dest\n)+ . Some mappings already exist in https://github.com/lindenb/jvarkit/blob/master/src/main/resources/chromnames/g1kv |
-i | if no mapping found, skip that record. |
-C | if no mapping found, use the original name instead of throwing an error. |
-h | get help (this screen) and exit. |
-v | print version and exit. |
-L (level) | log level. One of java.util.logging.Level . Optional. |
##Source Code
Main code:
##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
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
- 2013: Creation