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Understanding IGV

Hi

I have targeted sequencing (WGS)

I have uploaded bam and vcf file for sample; From these screenshot which one shows/support this mutation

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I am struggling to understand how to use bam file in IGV to see if reads support a mutation which passed the filter

Thanks for any help

vcf igv bam wgs
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updated by GenoMax GenoMax • written by zizigolu zizigolu

Why are there more than one screenshot if you are referring to a specific location? Which of the shots is supposed to be the location (you seem to be showing 1791something coordinates instead of 1792* per table)? You seem to have a large number of reads and IGV is likely downsampling the data. Have you checked that setting? Also use "Pack" setting to pack more reads in view.

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written by GenoMax GenoMax

I am very new to IGV I am not sure how to do that I took several screenshot because I do not know which part is the mutation I want

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written by zizigolu zizigolu

You can directly type in the coordinate you want to look at in the relevant box at the top e.g. chr1:179221102 that will put the coordinate dead center in the IGV window. You can then zoom out if needed.

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written by GenoMax GenoMax

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