Lindo Nkambule
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Recent activity by Lindo Nkambule Sort by recent activity-
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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Thank you! That fixed the issue.
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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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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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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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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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Hi GATK Team, I am checking in to see if someone has seen this issue?