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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

# Haplotype Caller -dcov flag

Member

Is there any way to override/re-implement the -dcov flag (which has been removed from the haplotype caller). I have a region that is almost 700 base pairs deep and continually causes a memory overload error. How can I restrict the coverage depth effectively?

Thanks,
-Paul

Tagged:

Hi Paul,

What version are you using? The -dcov` option is available in the current version, which is 2.6-4.

• Member

I am using GATK v2.5-2, maybe it is just the online documentation that is missing the -dcov discription, but I was unable to discern whether or not -dcov refers to the number of reads starting at a single location (i.e. -dcov = 2 would only allow 2 reads to begin at the same place), or if it refers to the number of reads at any location (i.e. -dcov =2 would only allow 2 reads to appear at a specific location in the genome).

Thanks,
-Paul

• Member

Perfect, thanks for the quick responses!