Anson Wong
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Activity overview
Latest activity by Anson Wong-
Anson Wong commented,
Hi Genevieve Brandt (she/her), You are right! Without the BAM input, the processing time is much faster now (> 500,000 variants per minute). According to the VariantAnnotator's documentation, "-I s...
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Anson Wong commented,
Hi Genevieve Brandt (she/her), Thank you for your suggestions. I started again VariantAnnotator commands (same as the one provided above) and tried both -Xmx8G and -Xmx16G, but their speed is the s...
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Anson Wong commented,
Hi Genevieve Brandt (she/her), it's HaplotypeCaller that only took 4 hours. Since VariantAnnotator has not been completed after running for > 1 day, I stopped it.
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Anson Wong commented,
Hi Genevieve Brandt (she/her), Thank you for your help. I did HaplotypeCaller for one WGS sample before running VariantAnnotator. I split the wgs_calling_regions.hg38.interval_list (provided by GAT...
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Anson Wong created a post,
GATK v4.2.4.0 VariantAnnotator running too slow
AnsweredHi all, I am running the latest GATK v4.2.4.0 VariantAnnotator, but similar to the problem mentioned in this post, the running speed is very slow (~5000 sites per min). The development team mention...