How can I visualize the Pileup to determine if there is a 5 BP deletion?
2
0
Entering edit mode
3.4 years ago
screadore ▴ 20

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 • 1.2k views
ADD COMMENT
1
Entering edit mode
3.4 years ago
GenoMax 142k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Perfect thank you very much!

ADD REPLY
1
Entering edit mode
3.4 years ago

Just adding an alternative answer for others:

samtools tview

Kevin

ADD COMMENT

Login before adding your answer.

Traffic: 1274 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6