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Output difference between HaplotypeCaller -ERC BP_RESOLUTION and mpileup
Output of HaplotypeCaller -ERC BP_RESOLUTION, as an intermediate vcf, records all non-reference allele in the vcf for downstream use. From where I see it, it is kind of like mpileup which records all non-reference position as well and both serves similar purpose. I am wondering if there are any difference in term of internal mechanism and output manifest?
P.S. The altimate goal is to creat a reference database of systematic artifact (all positions where false positive variants are likely to occur) and I am trying both HaplotypeCaller and mpileup