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Question: How To Split A Bam File By Chromosome
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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.

ADD COMMENTlink 7.7 years ago GPR • 320 • updated 2.1 years ago hewm2008 • 20
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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 7.7 years ago
Alex Paciorkowski
3.3k
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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 7.7 years ago
GPR
• 320
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bam != bedgraph, fyi.

ADD REPLYlink 7.7 years ago
Madelaine Gogol
5.1k
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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 7.7 years ago
GPR
• 320
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Try samtools reheader to get the header back.

ADD REPLYlink 7.7 years ago
Michael Dondrup
46k
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@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 7.7 years ago
Madelaine Gogol
5.1k
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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 6.8 years ago Jorge Amigo 11k
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This has the advantage of only generating a bamfile for the reference that you want.

ADD REPLYlink 2.4 years ago
russ.bainer
• 0
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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 2.0 years ago
mg
• 30
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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 7.7 years ago Michael Dondrup 46k
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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 5.4 years ago
travcollier
• 160
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A solution would be converting bam to fastq file, then use the fastq to map to specific chromosome

ADD REPLYlink 3.8 years ago
Chen
• 880
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This is silly as it's slow and the file wouldn't be indexed.

ADD REPLYlink 3.7 years ago
SmallChess
• 480
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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 19 months ago
uribe.convers
• 0
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I would try the bamtools way (Jorge Amigo's answer) instead. It might be possible to parse and filter the entries going through text format, but it can also easily mess up everything.

ADD REPLYlink 8 months ago
Michael Dondrup
46k
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samtools view in.bam chr1 -b > out.bam use -b to output bam format

ADD COMMENTlink 6.6 years ago SHI Quan • 80
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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 6.8 years ago Pierre Lindenbaum 120k
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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 4.1 years ago Shicheng Guo ♦ 7.5k
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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 4.1 years ago
Jorge Amigo
11k
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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 22 months ago
goodez
• 460
0
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This soft can help all of you

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

ADD COMMENTlink 2.1 years ago hewm2008 • 20

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