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can depth of bam file at some position is lower than depth of vcf?
I aligned reads to reference with BWA-mem and called variants using HC.
In my understanding, depth of bam can be reduced in vcf file because of some filtering options. However, can depth of bam file at some position is lower than depth of vcf? for example, in a bam file, there is only one read is aligned to reference. reference is G and alternative is A. So, if I understand about variant calling, AD should be 0:1, isn't it? But AD is 0:2. How can I interpreter this situation?
I want to upload my files but I cannot open the attach image option above.