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I have a bam-file of reads and reference genome. How can I located matches, mismatches and indels in three different files with Phred score in each data of the files?

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Try one of these:

GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4

freebayes: https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-dnaseq-workflow.html#gsc.tab=0

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