Layne Sadler
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Activity overview
Latest activity by Layne Sadler-
Layne Sadler commented,
Broader ARM thread:https://gatk.broadinstitute.org/hc/en-us/community/posts/5462468688539-Is-ARM64-Linux-MacOS-architecture-officially-supported?page=1#community_comment_24767487506459
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Layne Sadler commented,
Soon ARM compatibility is going to become a bigger issue than supporting macOS. Windows computer manufacturers will be switching to Qualcomm ARM by default. AWS is offering ARM servers.
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Layne Sadler commented,
GATK should issue a warning when allosomes are detected without using appropriate ploidy options
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Layne Sadler commented,
This is what I see for the chrX genotypes of a randomly selected male GT:count1/1:17020/1:3711/2:14 Consider that GQ>=15 means 95% confidence --- chrY is worse because the majority are labeled het...
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Layne Sadler commented,
Make sure that vcf tools is actually applying your filters. In high depth samples, lots of low quality variants creep in: https://www.biostars.org/p/9564606/
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Layne Sadler created a post,
Do GATK tools support Apple silicon?
I need to purchase a new laptop. I want to upgrade to a many-cored Mac with the new Apple silicon chips for parallelism, speed, and reduced power consumption. This is especially attractive for vari...
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Layne Sadler commented,
Does HaplotypeCaller support Apple silicon?https://www.biostars.org/p/478429/#495387
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Layne Sadler commented,
Here is a table comparing Funcotator to VEP variant classifications. It's not completely 1-1 as some of the high/moderate are missing. https://docs.google.com/document/d/1Xplvq-6wNUKQWUN7hsNPu_TFdy...
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Layne Sadler commented,
Agreed that the annotations should have their own page to be more searchable
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Layne Sadler commented,
So I got this running (hope it finishes) after a few hours of troubleshooting. It would be nice to have links to information about upstream steps like generating the supplemental files like the fas...