If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
VariantRecalibratior questions; no plot shown in .R.PDF
1) When I used UnifiedGenotyper and VariantRecalibrator to analyze“NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam” downloaded from bundle, I can get right format VCF (98447 SNP) and “.R.PDF” that appeared to show right plots.
2) However, using the same approach to analyze my own 8 recalibrated bam files (target re-sequencing project, I can only obtain right format VCF (2654 SNPs), but with the error message followed by VariantRecalibrator:
ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider raising the number of variants used to train the negative model (via --percentBadVariants 0.05, for example) or lowering the maximum number of Gaussians to use in the model (via --maxGaussians 4, for example)
3) In order to test whether I can use recalibration step, first I run UnifiedGenotyper by combining all my recalibrated Bam files and NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam file together and got right format VCF (101540 SNP) ). Then, I run VariantRecalibrator: this time, there is no error message, but R.PDF file didn't show plots.
Could you explain what might happen?