I am using Unified Genotyper for SNP calling. I find that the reported Allele depths and read depths seem much lower than expected (with and without the base quality recalibration). I did the alignment using CLC bio and have a SNP file from CLC bio which reports the coverage at the SNP position of reads that passed the quality filter. I understand the reported coverage values may not be exact but for equivalent quality scores, I find the DP from GATK to be 10% or 20% of the CLC bio coverage. Has anyone else seen this? Does GATK scale down the coverage?
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