Question: sugesstions to optimize an abra2 command
0
gravatar for bioguy24
5 days ago by
bioguy24190
Chicago
bioguy24190 wrote:

Looking to speed up abra2 and added libIntelDeflater.so and --threads 8/16. I am running diploid germline but don't see how to adjust the pruning to .10 as suggested. Anything else? Thank you :).

java -Xmx16G -jar $abra -Dsamjdk.intel_deflater_so_path=</path/to/libIntelDeflater.so> --in <bam> --out <abra.bam> --ref <fasta> --threads 8 --targets <bed>
abra2 • 59 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by bioguy24190
1

Since this is not a very commonly referred to program here you may want to write to program author to get an answer. Please post here, if you do get a reply.

ADD REPLYlink written 5 days ago by genomax76k

Thank you very much :).

ADD REPLYlink written 4 days ago by bioguy24190
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