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Indel Genotypes
The variant caller filters all bases marked by the mismatch density filter and any N base calls that remain after the end-trimming step. These filtered base calls are not used for site-genotyping but appear in the filtered base call counts in the variant caller output for each site.
All remaining base calls are used for site-genotyping. The genotyping method heuristically adjusts the joint error probability that is calculated from multiple observations of the same allele on each strand of the genome. This correction accounts for the possibility of error dependencies.
This method treats the highest-quality base call from each allele and strand as an independent observation and leaves the associated base call quality scores unmodified. Quality scores for subsequent base calls for each allele and strand are then adjusted. This adjustment increases the joint error probability of the given allele above the error expected from independent base call observations.