Question: How To Filter Bam File
8
gravatar for Junfeng
9.3 years ago by
Junfeng330
Junfeng330 wrote:

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 • 19k views
ADD COMMENTlink written 9.3 years ago by Junfeng330
17
gravatar for brentp
9.3 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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.

ADD COMMENTlink modified 9 months ago by RamRS27k • written 9.3 years ago by brentp23k

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

ADD REPLYlink written 9.3 years ago by Junfeng330
2
gravatar for iw9oel_ad
9.3 years ago by
iw9oel_ad6.1k
iw9oel_ad6.1k wrote:

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.

ADD COMMENTlink written 9.3 years ago by iw9oel_ad6.1k

Thanks for telling me such a useful software.

ADD REPLYlink written 9.3 years ago by Junfeng330
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