Comments (4)
lbergelson
commented on August 21, 2024
That's worrisome. We've never enabled the optimized smith waterman by default in GATK because of some other issues, but I hadn't ever seen it produce grossly incorrect alignments. I was under the impression that it had been tested pretty heavily against the GATK java implementation. I wonder if we produce the same bad alignment...
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lbergelson
commented on August 21, 2024
I'm confused about this one. Running this code against the GATK java smith waterman implementation produces the same result. It seems to have something to do with the overhang strategy although none of the overhang strategies produce the answer that seems most correct. @davidbenjamin do you have any sense of what's going on here?
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davidbenjamin
commented on August 21, 2024
@lbergelson See comments in broadinstitute/gatk#6576.
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Kmannth
commented on August 21, 2024
Still blocked on broadinstitute/gatk#6576
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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
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