Extracting frequency allele threshold information.

[Jane Wilson]

Hello,

  I was wondering if there is any way of extracting the information about mutations/deviations in the two pop-up windows in the screen shot below.  We are analysing viral genomes, and would like to plot the percentage per site in the genome of all deviations from the reference (insertions + deletions + nucleotide changes).

If you had any advice on how to extract this information, I’d be very grateful!  We are using Illumina HiSeq data, mapped to the reference using bowtie or BWA.

Thanks very much,

Jane

[Jim Robinson]

Hi,

No, unfortunately there is not.  IGV is primarily a visualizer, we leave analysis to other tools (samtools, bedtools, Picard, ...).   One could argue this simple counting is not analysis, but you can't do it currently.  You can use igvtools to count nucleotides by position, but that does not get you all the way.

I suggest you look at samtools mpileup to see what it has, and maybe post your question more broadly in nextgen analysis forums.

Jim

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[Jane Wilson]

Hi Jim,

  thanks very much for your reply.  I'll look into mpileup.
Thanks again,

Jane

[Rafael Kroon Campos]

Hello,

I have a similar question, but I just want the count per nucleotide. When I hover over my data with the mouse in IGV I can see the total count for each nucleotide in the reference sequence. Is it possible to export this data in a list format to excel so I could have the total count in one column and each nucleotide of the reference sequence in another? The viral genome I am looking at is 11000 bases long.

For example:

A- total count= 300

T-total count= 500

G- total count =500

A= total count =550

 thank you,

Rafael Campos 

[Jim Robinson]

Hi,

You can do this with igvtools from the command line, see the user documentation for the "count" command. 

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