I use a bed to find mutations and use the mutect2 process. Normal samples and tumor samples use mutect2 for mutation detection. After importing the bam file of bqsr into IGV, I found that this site has a difference in mutation multiples between normal and tumor samples. But this mutation cannot be found when mutect2.bam is imported into IGV. why？
Then use another bed to find the mutation..it can be found in mutect2.bam Why is this happening? Both beds contain the location of the mutation
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