Comments (2)
gspowley
commented on August 21, 2024
@mepowers, can you please respond to this request?
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rpomaris
commented on August 21, 2024
@rick-heig - I missed this notification - my apologies.
Our team specifically doesn't have plans to take on new FPGA development work, but I know our FPGA product group is still working in genomics, and we have active external collaborations in this space. @aprabhak2 - please feel free to chime in if you have input here.
It looks like HaplotypeCaller can be run with a doubleprecision flag for pairHMM: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php
... and doing so "is slower but matches the java implementation better."
For the FPGA implementation of pairHMM, I would expect similar results, ie slower but better matching the java implementation. I'll let @aprabhak2 correct if that's wrong.
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Related Issues (20)
- How to make the system use these libraries? HOT 1
- GATK4 HaplotypeCaller native SmithWaterman: core dumps and JVM errors HOT 2
- Intermittent core dump in native pair hmm HOT 5
- Does GKL have plans to support ARM architecture optimization? HOT 2
- Help2man is also needed when building. HOT 2
- PairHMM stripe initialization of `M_t_1_y` is wrong HOT 1
- GKL uses exploitable Log4J 2 version HOT 1
- GKL should ideally use commons-logging or similar instead of log4j HOT 2
- `smithWatermanBackTrack` is being shared between AVX2 and AVX-512 HOT 2
- Release 0.8.9 is not on maven HOT 3
- Potential memory leak observed in unusual HaplotypeCaller behavior HOT 1
- Help, where is the function impl of 'compute_fp_avx512s' ?
- Does GKL support arm architecture? HOT 2
- Confusing warning message in IntelInflater HOT 1
- IntelDeflater intermittently fails to properly compress outputs with GKL 0.8.8 HOT 3
- Segfault in the native PairHMM on certain CPU / JVM combinations
- Deflater.needsInput() Always returns true HOT 4
- the way of docker or apptainer install
- GATK AVX accelerated pairHMM Segfault issue with Long reads - Consistently around the same region
- SmithWaterman result inconsistency by optimization level
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