Counting number of mutations per read compared to reference
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5 weeks ago
x_ma_x • 0

Apologies if question is basic, but I'm very new to NGS analysis!

I have some Miseq DNA sequencing data (in .fastq format) which I can align to sam/bam. What I would like to get from this data is how many mutations (if any) there are for every read, and ideally also the type of mutations present in every read. In other words, some quantitative measure of sequence similarity. What's the easiest way of getting such data? The objective is to assess random mutagenesis efficiency.

As an extra, I'd like to get same data but after translation of my sequence into protein (to detect nonsense/silent mutations etc.

mutation bam ngs • 138 views
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@Pierre has a tool that does this: http://lindenb.github.io/jvarkit/Sam2Tsv.html

You will need to annotate the VCF/SNP's independently to get the information about effects of those SNP.

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