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BamRenameChromosomes

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Pierre Lindenbaum edited this page Dec 17, 2013 · 5 revisions

##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:

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

##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

##History

  • 2013: Creation

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