Splitting paired end bam files
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7.2 years ago

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 rna-seq next-gen • 3.5k views
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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.

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7.2 years ago
Dan D 7.3k

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

outputting to a named pipe

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