Question: Splitting paired end bam files
gravatar for tharveshliyakat
5.5 years ago by
tharveshliyakat60 wrote:

Hello all,

Any efficient way to split the bam file to two separate files, say one file with only singletons(mate unmapped) and other with paired reads(no matter if it is discordant).

I have already used.

(i) samtools view -f 8 -F 4 -b foo.bam > foo.singletons.bam

(ii) samtools view -f 1 -F 12 -b foo.bam > foo.paired.bam

Is this correct solution to go ahead.

PS: This file has already been filtered for uniquely mapped reads using NH:i:1 tags.

rna-seq next-gen • 2.9k views
ADD COMMENTlink modified 5.5 years ago by Dan D7.1k • written 5.5 years ago by tharveshliyakat60

if you -f 1 to the second command, you should really -f 9 to the first to be fair :)
Even though its unlikely youll ever come across a bam file with both single reads and paired reads, the first command would match both. The single reads it would match would also be pretty random - not all of them.

ADD REPLYlink written 5.5 years ago by John12k
gravatar for Dan D
5.5 years ago by
Dan D7.1k
Dan D7.1k wrote:

That looks good to me. To save space, you might also try outputting to a named pipe:

outputting to a named pipe

ADD COMMENTlink modified 14 months ago by _r_am32k • written 5.5 years ago by Dan D7.1k
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