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something fishy? VCF depth and BAM depth don't match
So after performing a multisample variant calling using GATK 126.96.36.199, I separated one of the samples and wanted to visualize one heterozygous site on IGV. If you see from the attached image, the VCF shows that the Depth is 1 and the GQ is 99. But, the BAM file has lots of reads assigned to that position. I have used the original BAM file that was used during the variant calling. Is there a possibility of rearrangement at that site due to which the Depth became 1? Should have I used the rearranged BAM file instead for visualizing? If the Depth is 1 in the VCF file, how come the GQ is 99?