Hello- I am attempting to perform BQSR as the final step of the GATK work flow for processing exome capture data prior to calling SNPs. The data are from a non-model organism (mosquito), so we are using the "bootstrapping" approach to generate the recalibration table by providing a vcf with known variants. We've done this twice with two sets of known variants: 1) known SNPs from previous RNAseq experiments, and 2) a conservative set of SNPs from the data we are trying to recalibrate. In both cases, the recalibration drastically reduces the quality scores. Pre-recalibration scores are in the 36-40 range, post-recalibration scores are in the 18-20 range. I can post the recalibration tables if that would be helpful. We are using GATK version 3.6 and the quality score encoding is Sanger/Illumina 1.9. Thank you very much for any suggestions about where we might be going wrong!
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