How To Filter Bam File
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10.2 years ago
Junfeng ▴ 330

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.

filter • 21k views
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10.2 years ago
brentp 23k

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.

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

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2
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10.2 years ago

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.

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Thanks for telling me such a useful software.

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