Lindo Nkambule
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Activity overview
Latest activity by Lindo Nkambule-
Lindo Nkambule created a post,
ApplyVQSR output restriction
AnsweredHi GATK Team, I'd like to know if it possible to restrict the output to within a specific interval? I am running ApplyVQSR and supplying an interval file with the interval chr1 111057913 117227796 ...
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Lindo Nkambule commented,
Hi Genevieve Brandt (she/her) and Samuel Lee Apologies for the late response. My primary goal was to write this pipeline here in Hail Batch and the defaults are 75 for SNPs and 10 for INDELs, I hav...
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Lindo Nkambule commented,
Thank you! That fixed the issue.
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Lindo Nkambule created a post,
ArrayList cannot be cast to String in VariantRecalibrator
AnsweredHi GATK team and community, I've encountered an java.util.ArrayList cannot be cast to java.lang.String error while trying to run VariantRecalibrator GATK version used: 4.2.6.1 Exact command used...
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Lindo Nkambule commented,
Hi Genevieve Brandt (she/her), that was the case. Running the command without -an AS_SOR doesn't give issues. Thank you!
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Lindo Nkambule commented,
Sure! Below is the command: gatk --java-options "-Xms118g -XX:+UseParallelGC -XX:ParallelGCThreads=14" \ VariantRecalibrator \ -V gs://hgdp-1kg/vqsr_pipeline/gnomad_genomes_v3.1_info.vcf.bgz \ ...
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Lindo Nkambule commented,
The VCF was created by the gnomAD team and it's not yet public unfortunately, I am using it for testing a pipeline. I am not sure which software was used to generate the VCF but I'm almost certain ...
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Lindo Nkambule commented,
Hi Genevieve Brandt (she/her) I've tried using ValidateVariants but it doesn't output anything. This is what I get 14:17:33.276 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:...
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Lindo Nkambule commented,
Hi GATK Team, I am checking in to see if someone has seen this issue?
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Lindo Nkambule created a post,
VariantRecalibrator IndexOutOfBoundsException
AnsweredHi GATK team and community, I've encountered an IndexOutOfBoundsException error while trying to run VariantRecalibrator GATK version used: 4.2.6.1 Exact command used: gatk --java-options -Xms{java_...