merging tdf files

[Christophe Klopp]

Hi,

We have multiple large bam files for the same samples and would like
to visualize the depth for each sample in IGV without having to merge
the bam files. Is it possible to merge the tdf files?

Cheers

Christophe

[Jim Robinson]

Hi,

Not its not, but that would be a good feature. The next release of
igvtools is in development, we will try to include a solution to this
with that release.

Jim

[James Robinson]

Hi Christophe,

Apologies if we haven't gotten back to you on this. Its not possible to merge tdf files, however you can logically merge these bams as input to the "count" command by creating a ".bam.list" file, and using this as the input file. The file is simply a list of bam files, one per line, with an extension ".bam.list". This option works for the "early access" igvtools, available here:

http://www.broadinstitute.org/igv/projects/downloads/igvtools_test.zip

or

http://www.broadinstitute.org/igv/projects/downloads/igvtools_nogenomes_test.zip

-- Jim