Question: How To Split A Bam File By Chromosome
5
gravatar for GPR
6.4 years ago by
GPR310
Mexico
GPR310 wrote:

Hello, I am having a hard time opening a very large bedgraph. I have been suggested to split my bam file by chromosome with chrom-bed.py but it didn't work. Is there any other alternative? Thanks, GP.

bam split chromosome • 41k views
ADD COMMENTlink modified 8 months ago by hewm200810 • written 6.4 years ago by GPR310
1

How are you having a hard time opening the file? What happens? How did your script to split the bam file "not work"? These details may help people answer your question.

ADD REPLYlink written 6.4 years ago by Alex Paciorkowski3.3k

I am pretty much having trouble with the indexing and header of my bam file. I have indexed in various ways, but keep having trouble. Have tried chrom-bed.py and samtools view chr1 > chr1.bam. I have indexed with samtools and bamtools, I even tried sorting the file before indexing. Any suggestions?

ADD REPLYlink written 6.4 years ago by GPR310
1

bam != bedgraph, fyi.

ADD REPLYlink written 6.4 years ago by Madelaine Gogol5.0k

I have indexed and when running samtools virew, I get the message fail to read the header from bam file. Any tips?

@ Madelaine: yes I have converted my bam files to bedgraph ones successfully. The problem is the size, that's why I want to split them by chromosome

ADD REPLYlink written 6.4 years ago by GPR310

Try samtools reheader to get the header back.

ADD REPLYlink written 6.4 years ago by Michael Dondrup44k

@genaro Oh, sorry.

You can also use picard CreateSequenceDictionary on the genome fasta and add that to the top of the sam file if the sam file is missing a header.

ADD REPLYlink written 6.4 years ago by Madelaine Gogol5.0k
18
gravatar for Jorge Amigo
5.5 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

in this other answer, Aaron Quinlan stated:

bamtools has a "split" command for exactly this purpose

I can only add that I've just tried it with this simple command

bamtools split -in file.bam -reference

and it works like a charm. the bam file gets split into different bam files, which are suffixed with .REF_xxx.bam by default, which is very convenient.

ADD COMMENTlink written 5.5 years ago by Jorge Amigo11k

This has the advantage of only generating a bamfile for the reference that you want.

ADD REPLYlink written 12 months ago by russ.bainer0

Is it possible to specify output directory, and to mention which specify chromosome needs to be extracted (for eg., just chr5 and chr22)?

ADD REPLYlink modified 7 months ago • written 7 months ago by mg20
11
gravatar for Michael Dondrup
6.4 years ago by
Bergen, Norway
Michael Dondrup44k wrote:

Try samtools: samtools view -?

A region should be presented in one of the following formats: chr1',chr2:1,000' and `chr3:1000-2,000'. When a region is specified, the input alignment file must be an indexed BAM file.

something like samtools view in.bam chr1 > chr1.bam should work

ADD COMMENTlink written 6.4 years ago by Michael Dondrup44k
6

You're missing the '-b' flag (bam output).  So something like:

​samtools view -b in.bam chr1 > in_chr1.bam

NOTE: The sequence dictionary (@SQ header lines) will still contain entries for everything.  This can cause problems if the tools you're feeding those split bam files into use that header information.  For example, picard CollectWgsMetrics will still assume that the bam is supposed to cover the whole genome, not just a single chrom.  I'm certain lots of other tools will have similar problems.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by travcollier140

A solution would be converting bam to fastq file, then use the fastq to map to specific chromosome

ADD REPLYlink written 2.4 years ago by Chen730

This is silly as it's slow and the file wouldn't be indexed.

ADD REPLYlink written 2.3 years ago by SmallChess460

Is there a way to prevent each bam file to have entries for everything in the sequence dictionary (@SQ)? Or is there a way to recreate/parse/filter the header for each specific bam?

ADD REPLYlink written 10 weeks ago by uribe.convers0
7
gravatar for SHI Quan
5.2 years ago by
SHI Quan70
shenzhen
SHI Quan70 wrote:

samtools view in.bam chr1 -b > out.bam use -b to output bam format

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by SHI Quan70
6
gravatar for Pierre Lindenbaum
5.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

I wrote a java tool to split a BAM per chromosome see http://code.google.com/p/jvarkit/wiki/SplitBam

It also creates an empty BAM (filled with a pair of mock SAMRecords) for each chromosome in the Reference, if no SAMRecord was found for the chromosome.

ADD COMMENTlink written 5.5 years ago by Pierre Lindenbaum112k
2
gravatar for Shicheng Guo
2.7 years ago by
Shicheng Guo6.9k
Shicheng Guo6.9k wrote:

You can use the following pipeline to extract chrY reads from the raw bam files and with the header

samtools sort A.bam -o A.sort.bam
samtools index A.sort.bam
samtools view -H A.sort.bam > output.extraction.sam
samtools view A.sort.bam chrY >> output.extraction.sam
samtools view -hb output.extraction.sam > output.extraction.bam
samtools view  -H output.extraction.bam 

output.extraction.bam is the bam file which extracted chrY reads.

 

 

 

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Shicheng Guo6.9k

this isn't really an answer to the original question.

plus if you want to extract chrY reads you only need a single command:

samtools view -b in.bam chrY > out.bam
ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Jorge Amigo11k

This is true but still requires a sorted and indexed bam file. From the samtools manual:

Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).

samtools sort A.bam -o A.sort.bam
samtools index A.sort.bam
samtools view -b A.sort.bam chrY > output.extraction.bam
ADD REPLYlink modified 5 months ago • written 5 months ago by goodez260
0
gravatar for hewm2008
8 months ago by
hewm200810
hewm200810 wrote:

This soft can help all of you

https://github.com/BGI-shenzhen/BamSplit

ADD COMMENTlink written 8 months ago by hewm200810
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