Answers.Body: <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>
  
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Body: <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>
  
Tags: <phylogenetics><indel><phred-scores>
Title: Matches, mismatches and indels
ThreadText: # Matches, mismatches and indels
  
  (Asked by: username_0 on 2022-11-28)
  
  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?
  
  **Tags:** phylogenetics, indel, phred-scores
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-11-28. Score: 4
  
  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>
  
  
  ---
  
  