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Test-drive the GATK tools and Best Practices pipelines on Terra
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GenomeSTRiP Sensitivity with bimodal library
We had a bimodal library in a bam file and tried to test how GenomeSTRiP handled the non-normal insert size distribution.
We spiked in a 1000 deletions with BamSurgeon into 4 RG (one of which was bimodal). Each RG had 10x coverage. We then created 3 bam files with 30x coverage (RG a,b,c), another with 40x (RG a,b,c,d) and another 30x (a,c,d). Library d was bimodal. We then ran GenomeSTRiP on these 3 bam files plus 47 other bam files.
Despite the differences in bam files, the sensitivity was exactly the same for the calls on each bam file. The same number of "truth" deletions were detected in each bam file. This was not the case in other programs we tested this on. Does this make sense with the population based approach? With GenomeSTRiP, is there a more appropriate way to test the impact of coverage or bimodal libaries? What would be the expected impact of a bimodal library on discovery and genotyping with GenomeSTRiP? Would it be better to remove the bimodal library or leave it in there for analysis?