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I just found the information in the Intel Paper : "Upon integration with the GATK Best Practices pipeline, the overall pipeline speed-up was 1.2x compared to the Intel AVX technology implementation." The actual speed-up is 1.2x compar…
That's too bad, didn't anyone try it at least ? From the intel paper : h ttps://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/wp/wp-accelerating-genomics-opencl-fpgas.pdf They say : 1) They have a much higher performance w…
@bhanuGandham thank you very much for your inquiry.
@AdelaideR Thank you for your response. I was suspecting this, seeing that the option was not available. The documentation is a bit out of sync with the version but it is good to know the option will be ported to the next version release. Best…
Sorry for the delay, The command I try to launch is : ``` $GATK HaplotypeCaller -R ref/ref.fasta -I bams/mother.bam -O sandbox/motherHC.vcf -bamout sandbox/motherHCdebug.bam --disable-optimizations --dont-trim-active-regions --force-active -…
Hello, thank you for your reply. The algorithm is clear to me, from what I read of the code it is effectively the right of figure 4.1 (or 4.2 without the start and end states for simplicity) that is used and not 4.3 Therefore my concern, the com…