I have bam files ~50Gb, which is read alignments onto a reference genome. now I want to extract some regions of alignment, but I found methods like samtools view -L region.bed all.bam
is too slow, usually taken more than 2 hours (even if very small region are submit)
Are there any other methods that can do this job faster?
6 answers
Extracting small regions from a bam file should be sub-seconds fast if the files are properly indexed. You don't say what version of samtools you are using (and I don't know if this is still an issue), but I recall that at least some point there was an issue where specifying the region on the command line
samtools view -h reads.bam 1:1042000-1042010
would use the index while specifying the -L option and providing a bed file of intervals would result in the entire file being read. You may try specifying an interval at the command line to see if that helps.
For only one position, it's the fastest way to do!
BEDtools is a good tip, but I would recommend intersectbed here:
intersectBed -abam reads.bam -b regions.bed > reads.regions.bam
or, if you want output in BED format
intersectBed -abam reads.bam -b regions -bed > reads.regions.bed
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written
by
David Langenberger
intersectBed -abam reads.bam -b regions.bed > reads.regions.bam will report original reads right ? How can i clip this reads to get just the part that overlap my intervals in the bed file ? thanks
See also this question & answer where @matted and myself compared samtools view -L with samtools view <region>. The latter is much faster. If you have several regions in file references.txt use (credit @matted):
cat references.txt | xargs samtools view -b input.bam > output.bam
My two cents:
samtools view -h reads.bam 1:1042000-1042010
If that doesn't work. try this:
samtools view -h reads.bam chr1:10420000-10421000
To output to another bam file format
samtools view -b reads.bam chr1:10420000-10421000 > subset.bam
Use Bedtools, it accepts BAM files!
bamToBed -i reads.bam > reads.bed
QuickBAM might be able to help, I think:
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Can you paste the header of your bam file (with
samtools view -H file.bam)