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I have a problem with the depth of coverage obtained after GATK workflow, which included indel realigner, baserecalibrator and unified genotyper. In the last vcf file the depth of coverage is very low (3-10), but if I check on IGV the bam file produced after alignment the reads count ranges between 70 and more than 100. Is it possible that the Baserecalibrator step reduce the read counts?
How can I manage this issue?
Thanks in advance