Question: Filter BAM app in Bam Tools
gravatar for lukacdm
22 months ago by
United States
lukacdm0 wrote:

I'm trying to eliminate inserts larger than 500 bp in a Bam file generated by Bowtie2 using the Filter BAM app in BAMTools (filter on insert size <=500). The largest read reported for the input Bam file is 81267 bp; hence, I want to delete all reads between 501 and 81267 bp. When I use the Picard tools to analyze insert sizes of the input and output files, the reported insert sizes are identical. I can't determine why Picard seems to see the large inserts, but BAM tools seems not to see them. Any help is appreciated.

More info via email: The data is ChIP-seq

insert size filter bam • 1.0k views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson24k • written 22 months ago by lukacdm0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:


If the datasets are the same size and generate the same stats, it doesn't seem that BAM Filter is actually doing anything.

I suggested double checking the filter syntax and re-running.

We are also running a few tests here. There was another reported problem with BAM Filter tool. More feedback after testing done, if the tool itself has a problem.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson24k

Update: From testing, Filter BAM tools is working correctly at for this function.

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson24k
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