Visualize variants and percentage of variants from one sample of Amplicon Seq data?

Visualize variants and percentage of variants from one sample of Amplicon Seq data?

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Hello,

We are analyzing viral evolution by analyzing mutations present in a specific genomic location and how it evolves over time. We are performing amplicon sequencing of a specific region that is 222-228 bp at intervals. There are two versions of the virus and 3 point mutations can cause a shift from virus A to virus B. For each sample I would like to create a chart that shows the variant sequence and then the percentage of that sequence within the reads.

I performed alignment to a fasta file with only two reference lines: the 222 bp of Virus A and the 228 of virus B using BWA. I then analyzed the percentage of reads that aligned to either reference.

I now am lost on how to get the output that I would like : (This image is from CRISPResso2 but I want something similar for non-CRISPR data)

enter image description here

I used GATK – haplotype caller to call variants but don’t know if that was the correct method to perform or if i should do multi-sequence alignment or something much more simple? I now have the VCF file from GATK but don’t know where to go from here.

Thank you for any advice,
Sara


Amplicon


PCR


RNAseq


GATK


BWA

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