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

Question

[screadore]

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!

Answer 1

[GenoMax]

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

[bernatgel]

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

[screadore]

Perfect thank you very much!

Answer 2

[Kevin Blighe]

Just adding an alternative answer for others:

samtools tview

Kevin