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Old 01-10-2013, 03:56 AM   #1
Location: Portugal

Join Date: Nov 2010
Posts: 11
Default Extremely high Coverage in some regions

Dear all,

I am currently working with NGS data for one individual sequenced using Illumina HiSeq 2000 (13-16x coverage).
I follow some standard pipelines to align and prepare the data for variant calling (BWA, Picard and GATK). (I am not interested in exome analysis but I've followed this pipeline to prepare the BAM files

When I was ready for the calling step I decided to check the coverage of this individual using BEDTools. The average coverage looks good (14/15X) but in some regions I get extremely high values like 9200x or higher !

I don't think that this is normal and I believe that these values are not OK even for repetitive regions...

Do you have any idea of what might be wrong?
Thank you all in advance,
JMFA is offline   Reply With Quote