SkyWarrior
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Activity overview
Latest activity by SkyWarrior-
SkyWarrior commented,
Hi @Yangyxt Can you check the capture metrics of your exome samples? Especially check zero coverage target percentage, AT dropout rate and GC dropout rate. Any obviously outlier samples will gi...
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SkyWarrior created a post,
Fontconfig error in the newest gatk docker image
AnsweredHi I just tried 4.2.6.0 docker image for germline CNV workflow and came across this error message in the logs. 08:57:35.253 DEBUG ScriptExecutor - --contig_ploidy_prior_table=/home/GATK_CNV/con...
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SkyWarrior commented,
Hi @Genevieve Brandt (she/her) I could not post any numbers today but I think I came up with a reason why systems are behaving differently. Storagewise AMD EPYC server has the fastest among all y...
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SkyWarrior commented,
Sorry they are not done yet. I will post them as soon as I get them.
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SkyWarrior commented,
Hi Genevieve Brandt (she/her) None of the systems have a compute level GPU present in fact I did not know that gCNV had a GPU support but that's besides the point. All systems that I use have at le...
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SkyWarrior created a post,
gCNV steps taking too long on server vs desktop pc.
AnsweredHi I would like to share an experience and ask a few questions regarding gCNV steps especially GermlineCNVCaller. I use different systems for gCNV workflows and I observe massive difference betwee...
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SkyWarrior commented,
Hi I saw this thread quite late but I need to add my own observations. 30 30X Whole genome samples on hg38 from NIST using only main contigs with non overlapping 1000base intervals excluding mask...
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SkyWarrior commented,
This issue is fixed with one of the later versions. I suggest you use 4.2.3.0.
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SkyWarrior commented,
Not really. Use IGV and compare the allelic imbalances from the short variants vcf and you should be set. Make sure that the changes that you track are not repeated in unrelated samples. Otherwise ...
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SkyWarrior commented,
I would recommend no less than 32 gb for 200k intervals with 30 samples. I would also recommend 4.2.2.1. 4.1.8.0 to 4.2.0.0 may have issues with skylake cpus xeon or not.