Use subBam from the BamBam package. Written in C. subBam -g targets.bed sorted.bam -o sorted.subset.bam -m 0
http://sourceforge.net/projects/bambam/ On Wed, May 6, 2015 at 4:23 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hi Roberto, > > Given the way BAM indexing works, I see no reason to actually > split the BAM file at all - it seems like wasted disk IO. > > Instead, can you split a BED file into sub-regions? This way > each child GATK job would look at the full BAM file but only for > a small region described in the split BED region file? > > Peter > > > On Wed, May 6, 2015 at 11:19 AM, Roberto Alonso CIPF <ralo...@cipf.es> > wrote: > > Hello, > > > > I have been working in the Galaxy parallelization module and I would > like to > > ask you some questions that I have about how to face one problem. > > I have done one pull request about splitting bams: > > https://github.com/galaxyproject/galaxy/pull/184 > > > > Regarding this, I think it is useful but it could be more while accessing > > somehow the interval. I better explain it with an example: > > If I define a simple tool like this, with the parallelism tag "actived": > > > > <tool id="gatk" name="call with gatk"> > > <description>gatk</description> > > <parallelism method="multi" split_mode="by_interval" > > split_size="100000000" merge_outputs="output" split_inputs="input" > >></parallelism> > > > > <command> > > ## by_rname > > ln -s $input input.bam; > > samtools index input.bam; > > UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/hg19_ucsc.fa -I > input.bam > > -o $output -L REGION ; > > > > </command> > > <inputs> > > <param format="bam" name="input" type="data" label="bam"/> > > </inputs> > > <outputs> > > <data format="vcf" name="output" /> > > </outputs> > > > > <help> > > bwa > > </help> > > </tool> > > > > The region is based on the field split_size, it is better explained in > the > > PR. > > How does the code from the PR work? It goes through the bam file and does > > something like "samtools view REGION -o bam_splitted.bam", so then GATK > does > > the calling for this small bam, but what is the problem? As you know, in > the > > software GATK if you don't pass the region as an argument in the command > > line it goes through all the genome, so it is very slow. So, what would > you > > recommend to me to be able to pass this information to GATK? I was > thinking > > to create, at the same time the bam is splitted, a file region.bed and > use > > it in the tool definition xml, so the command would be like this: > > <command> > > ... > > UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/hg19_ucsc.fa -I > input.bam > > -o $output -L region.bed; > > </command> > > > > This solution does not convince me too much because it is a bit > intrusive in > > the tool definition and also because you have to trust that the > region.bed > > file exists. > > Do you have any opinion, suggestion...? > > > > Thanks a lot! > > > > Best regards > > > > > > -- > > Roberto Alonso > > Functional Genomics Unit > > Bioinformatics and Genomics Department > > Prince Felipe Research Center (CIPF) > > C./Eduardo Primo Yúfera (Científic), nº 3 > > (junto Oceanografico) > > 46012 Valencia, Spain > > Tel: +34 963289680 Ext. 1021 > > Fax: +34 963289574 > > E-Mail: ralo...@cipf.es > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Joshua Udall (5133 LSB) Brigham Young University 701 E. University Parkway Plant and Wildlife Science Depart. Provo, UT 84602 Office: 801-422-9307
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