Question: (Closed) Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File
gravatar for Isaac Joseph
7.5 years ago by
Isaac Joseph100
Berkeley, CA USA
Isaac Joseph100 wrote:

Greetings all, The problem before me is as follows:

I have a pretty large .bam file, and from that file I need to find all mapping locations of a particular read name ("queryname" according to .bam lingo). Is there any way to do so efficiently? picard offers "FilterSamReads.jar", but this method is actually even slower than converting the .bam file to a .sam file and just using grep to extract reads with specific names.

In particular, one would imagine that one could take advantage of sorting the .bam file by queryname (using samtools sort -n) to do this efficiently in a similar manner to which one can extract all mappings to a particular reference in coordinate-sorted .bam files (produced by "samtools sort" within the -n option).

So, the main purpose of writing this is to verify that no efficient method actually exists before spending the time writing a new one.


picard samtools mapping bam sam • 17k views
ADD COMMENTlink modified 7.5 years ago by swbarnes28.6k • written 7.5 years ago by Isaac Joseph100

duplicate of

Extracting subsets of reads from a BAM file


ADD REPLYlink written 7.5 years ago by Pierre Lindenbaum130k

Ooh, good catch, thanks.

ADD REPLYlink written 7.5 years ago by Isaac Joseph100
gravatar for swbarnes2
7.5 years ago by
United States
swbarnes28.6k wrote:

Rather than making the .sam, you can pipe

samtools view file.bam | grep queryname - > subset.sam

That will save you the time of expanding a huge .bam file.

ADD COMMENTlink written 7.5 years ago by swbarnes28.6k

samtools view expands the huge .bam file though. That does, however, save hard disk space.

ADD REPLYlink written 4.0 years ago by Isaac Joseph100

Hi, how can I use this command for multiple reads of interest? Can I use a text file that has the read IDs and use grep on that text file?

ADD REPLYlink written 7 months ago by alhamidi.reem20
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