Question: Filter BAM app in Bam Tools
gravatar for lukacdm
2.6 years 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 • 1.5k views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by lukacdm0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k 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 2.6 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour