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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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