<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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2022-11-28T08:52:38.723Z
2022-11-28T08:52:38.723Z
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<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>

<phylogenetics><indel><phred-scores>
Matches, mismatches and indels
# 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

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## 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>


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