text: user16563: 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?
  
  user383: 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
  
original_text: 16563: <p>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?</p>
   383: <p>Try one of these:</p>
  <p>GATK:
  <a href="https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4" rel="nofollow noreferrer">https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4</a></p>
  <p>freebayes:
  <a href="https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-dnaseq-workflow.html#gsc.tab=0" rel="nofollow noreferrer">https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-dnaseq-workflow.html#gsc.tab=0</a></p>
  