I am working on amplicon data from an aploid genome (same length, already aligned with a miltiple alignment). Since I cannot generate a .bam file I ve to call mutations from aligned fastq through base count generation. To validate a mutation I ve to calculate genotype likelihood, but I cannot find a simplified version of the formula, despite I found a 'simpler' formula that expoites counter for GL calculation (https://gwct.github.io/referee/calcs.html). Moreover, all these formulae are not well explained in the page, so I am wondering if someone has already tryied to calculate GL by hand ( having base counts, base qualities and mapping qualities).
If possible, I would like to calculate GL in a 'samtools like' manner which is more conservative respect GATK and other tools.
