I constructed the variant calling pipeline for BAM file. However, when it was applied to positive samples, I did not find any well-known variants in the VCF file. What I am considering is that there might be less-sensitive method in my pipeline.
So I want to create a simulated BAM file based on the existed bam, just change the reads in the bam to create a variant, etc., rs6071.
Is there any convenient tool to do such, and also can I obtain a depth-aimed bam? For example, depth for alleles, A:G, 500:500, OR A:G, 800:200.