Make a deduplicated TDF file

[Alexander Predeus]

Hello all, 

I was wondering if there's a simple way to make a TDF file that's deduplicated. I do use TDF files extensively in my work with ChIP-seq experiments, but it's a bit misleading to look at TDF file with duplicates, especially if the duplication rate is substantial. 

If there are options other then make a deduplicated BAM/WIG and then convert it to TDF, I'd like to know about them.

Thank you in advance!

[Jim Robinson]

If the bam records are marked duplicate they will not be included in the coverage count (TDF file) by default.  You actually have to set a flag to include them.   See http://software.broadinstitute.org/software/igv/igvtools_commandline.

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[Alexander Predeus]

Jim,

So I do have to mark the duplicates as so first, with something like Picard or Samtools? 

What is the tool of choice here and what BAM flag do you mean exactly? 

Thank you for your help. 

-- Alex

[Jim Robinson]

Hi,

Yes, I'm referring to the "mark duplicates" flag. I think Picard can
do that, probably Samtools as well. See the SAM/BAM specification for
more details.

[Alexander Predeus]

Thank you for your help!