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Hello, When using the latest version of the GATK we observe a very small difference. We randomly sampled 1000 regions to call SNPs in, and when changing the default heterozygosity value to our barley value, we observe less than a 1% difference in t…
Thank you, I will try the latest version.
I understand the heterozygosity parameter, and the value that should be used. However, I am still unclear as to why decreasing the expectation of the number of differences between samples would increase the number of variants called. I would think t…
Thank you, we will try that and report back here.
We only have a set of about 8,000-9,000 known variants from a SNP genotyping array, and a handful of Sanger resequenced loci. Could this be a problem? Would calling SNPs, and using the high confidence variants in a second round of the BQSR help?
Thank you for the fast response. Attached are the plots generated from AnalyzeCovariates and our recalibration report. It looks like we have reads with reported qualities up to Phred40, but for some reason, they are being adjusted down to about Phre…