Number of non-duplicate-insert ALT reads (UNIQ_ALT_READ_COUNT)
Multiple reads with the same start position and fragment length are grouped and counted only once as they are likely duplicates. In most cases such reads should be filtered using a tool such as MarkDuplicates. This annotation is designed for use with unique molecular identifiers (UMIs), in which case reads with the same start and fragment length but different UMIs would appear to be independent. This is not a default annotation of any GATK tool but can be enabled on the command line with --annotation UniqueAltReadCount.
Although these reads have different UMIs, sometimes they really are PCR duplicates. We now believe that these duplicates are the result of a false-priming event that occurs during PCR amplification in which excess adapter remains after the ligation step and fails to be completely cleaned up during SPRI. This excess adapter is thought to act as a PCR primer during amplification, which leads to the synthesis of a molecule with the wrong UMI.
This annotation does not require or use any BAM file duplicate flags or UMI information, just the read alignments.
GATK version 188.8.131.52 built at Wed, 30 Jan 2019 10:21:04 +0530.