Display fraction of mutations and variants for Amplicon Sequencing sample?
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7 days ago
Saran ▴ 20


I have several Paired-End, Amplicon Sequenced data. The amplicon is 222 base-pairs and 2x250 sequencing was done so there is heavy overlap. I already aligned these sequences to the reference amplicon using BWA and created weblogos to display any regions with mutations.

I would like to do more analysis including:

  • Get fraction of mutated alignments versus wildtype
  • Display all of the different variants and their fraction within the pool of reads.

I can't find information online to tackle this issue. I would like to make an allele frequency table, listing all of the variant sequences and displaying the mutations. I am not sure if I am using the correct vocabulary and that is why I can't find the solutions that I am searching for.

I created VCF files from the bam files and am trying to investigate what I can do with these.

Any guidance would be appreciated. Thank You, Sara

PCR Amplicon VCF BWA • 77 views

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