HaplotypeCaller -ERC BP_RESOLUTION, as an intermediate vcf, record all non-reference allele in the vcf. From where I see it, it is kind of like mpileup which records all non-reference position as well. If I run both tools on the same sample, what kind of difference should I expect to see ?
P.S. The altimate goal is to creat a reference database of systematic artifact (all positions where false positive variants are likely to occur)