How To Filter Bam File

Question

[Junfeng]

Hi, I have one BAM file which contains all alignments (include those not used in variant calling, such as non-PF, non-mapping and duplicate reads) generated for an assembly. How to filter these useless mapping? I know that Picard MarkDuplicates can be used to remove duplicates.Thank you.

Answer 1

[brentp]

You can use samtools to do this. e.g. to remove reads that did not align, you can do:

samtools view -F 0x04 -b in.bam > out.aligned.bam

to only include paired reads, use:

-f 0x02

Check the other bitwise flags on this page.

But you might not want to exclude those as they could be used for finding structural variations.

[Junfeng]

Thank you. Your answer is very useful, I will try it.

Answer 2

[biobot 0.0.77.a.1099]

The bamtools package offers a wide range of filters, including user-definable filters defined in JSON notation. It includes filters for reads failing vendor QC, unmapped reads and pre-marked duplicates.

[Junfeng]

Thanks for telling me such a useful software.