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EHC 10-06-2011 11:27 AM

Dindel SAM/BAM format - viewing with IGV

I would like to get the SAM or BAM files of the events I got in the variantCalls.VCF final file. I use --processRealignedBA and then screen the bam files for the ones with the relevant window. Is there a way to produce bam files only for area I am interested in?

Also I failed to make the BAM files useful to view iGV (they look empty). Anyone has an idea why?


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