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Old 10-18-2020, 01:39 AM   #1
gamabunta313
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Location: Italy

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Default Calculate Genotype Likelihood from raw data

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 tryed 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
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