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Test-drive the GATK tools and Best Practices pipelines on Terra
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Deep sequencing data is missing variants in M2 called vcf
--max-reads-per-alignment-start is helpful because the genome has a few hotspots of extremely high coverage, due to mapping error for the most part, where to avoid spending an inordinate amount of compute on these few regions we truncated the coverage. For example, a 100x exome may have a few thousand bp with 10,000x coverage.
However, this behavior should be turned off, by setting --max-reads-per-alignment-start 0 , when the coverage is uniformly high and one wants to use that depth to discover low-AF variants.