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How can I visualize the Pileup to determine if there is a 5 BP deletion?

Hello everyone,

I'm currently trying to visualize the pileup of a sample to determine if there is a 5 Base Pair deletion and if there is another deletion 1 Base pair down stream.

I have access to the following files for the sample: - FastQ - Bam - Bam.bai - Pileup.txt - VCF

I have access to BaseSpace by Illumina, Galaxy, and IGV.

Could anyone tell me how to visualize these alignments and how to see the pileup. I just need to know what files and what tools to use. It would be very much appreciated. Thank you for any help!

sequencing genome sequence alignment
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updated by Kevin Blighe Kevin Blighe • written by screadore • screadore

2 answers

igv should be the easiest. A user guide for IGV is available.

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written by GenoMax GenoMax

and load the BAM file in there (maybe the VCF too so you can easily fin the variant you want), but the BAM will give you the pileup

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written by bernatgel bernatgel

Just adding an alternative answer for others:

samtools tview

Kevin

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written by Kevin Blighe Kevin Blighe

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