sugesstions to optimize an abra2 command
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>
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Thank you very much :).