ShiftBam

shit all coordinates of a bam

Usage

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

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

Usage: shiftbam [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --bed
      Bed Path. Extract Reads overlaping this BED. Or use -R2.
    -R2, --destination-reference
      Original fasta reference. We shift the bam back to this reference. 
      Required without --bed
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    -R, --reference, --source-reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --stringency
      Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit

Keywords

• bam
• sam
• bed

Creation Date

20241001

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/shiftbam/ShiftBam.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 shiftbam ? 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

shift coordinates of a BAM.

Usage 1

Say the bam has been mapped on a sub-fasta.

# here all contigs look like "chrxxx:123-456"
samtools faidx ref.fa "chr1:2345-6789" >  ref2.fa
samtools faidx ref.fa "chr21:12345-16789" >>  ref2.fa




(...)
bwa mem ref2.fa read1.fq read2.fq |\
    java -jar dist/jvarkit.jar shiftbam -R2 ref.Fa

````


In this sub-fasta all the chromosomes NAMES **MUST** look like 'chr1:123-456'.
This tool takes as input the original REF and the bam and it's coordinates in the new ref
and shit the coordinates to the new reference, including the SA:Z attributes.
Ouput BAM is not sorted on coordinate.


## Usage 2

we're creating a mini-genome containing the gene of interest using ROI.bed

java -jar dist/jvarkit.jar shiftbam --bed ROI.bed in.bam

## Example:

the following Makefile extract a BAM to a sub-region, call delly on a smaller REF, convert back the vcf to the original ref

```makefile
OUTDIR=work
PREFIX=myexperiment.
REF=ref.fa
BAM=${HOME}/jeter.bam
INTERVAL=chr1:123-456

$(OUTDIR)/$(PREFIX).shift.vcf: $(OUTDIR)/$(PREFIX).call.bcf
    bcftools view $< | java -jar $${JVARKIT_DIST}/jvarkit.jar shiftvcf -R2 $(REF) > $@

$(OUTDIR)/$(PREFIX).call.bcf : $(OUTDIR)/shift.01.bam $(OUTDIR)/shift.01.bam $(OUTDIR)/shift.ref.fa $(OUTDIR)/shift.ref.fa.fai $(OUTDIR)/delly
    $(OUTDIR)/delly call -g $(OUTDIR)/shift.ref.fa -o $@ $(OUTDIR)/shift.01.bam


$(OUTDIR)/delly :
    mkdir -p $(dir $@)
    wget -O "$@" "https://github.com/dellytools/delly/releases/download/v1.3.1/delly_v1.3.1_linux_x86_64bit"
    chmod +x $@

$(OUTDIR)/shift.01.bam: $(BAM) $(OUTDIR)/locus.bed
    samtools view -M -L  $(OUTDIR)/locus.bed -O BAM $(BAM)  |\
    java -jar $${JVARKIT_DIST}/jvarkit.jar shiftbam  --bed  $(OUTDIR)/locus.bed |\
    samtools sort -T $(OUTDIR)/tmp --write-index -O BAM -o $@

$(OUTDIR)/shift.ref.dict: $(OUTDIR)/shift.ref.fa
    samtools dict $< > $@

$(OUTDIR)/shift.ref.fa.fai: $(OUTDIR)/shift.ref.fa
    samtools faidx $<

$(OUTDIR)/shift.ref.fa : $(REF)
    mkdir -p $(dir $@)
    samtools faidx $< $(INTERVAL) > $@

$(OUTDIR)/locus.bed:
    mkdir -p $(dir $@)
    echo '$(INTERVAL)' | awk -F '[:-]' '{printf("%s\t%d\t%s\n",$$1,int($$2)-1,$$3);}' > $@