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Question: To varscan mpileup data
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gravatar for kuick77
2.5 years ago by
kuick77 • 10
kuick77 • 10 wrote:

HI, I have run the mpileup (process is completed and successful), and was trying to analyse the pile up data using Varscan, but why i didnt see any pileup dataset for me to choose in Varscan analysis tool?
tophat • 1.0k views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by kuick77 • 10

Did you make sure that you generated a pileup dataset? The default is VCF.

ADD REPLY • link written 2.5 years ago by bryantl • 90

Yes bryantl and thanks for your reply.

It generated two files, one is vcf , another is log file (both shown in green). I can view the vcf file in the galaxy. But when I proceed to use Varscan, there is no option for me to pick this vcf file.. I am puzzled.

ADD REPLY • link written 2.5 years ago by kuick77 • 10
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gravatar for bryantl
2.5 years ago by
bryantl • 90
United States
bryantl • 90 wrote:

A pileup dataset and a VCF are two different file types. Varscan is acutally using the pileup dataset to produce a VCF, so you may want to look at the VCF mpileup generated to determine if you need Varscan at all. If you want to use Varscan, you can get a pileup dataset from mpileup by selecting "Do not perform genotype liklihood computation" in the Genotype Likelihood Computation dropdown menu.

ADD COMMENT • link modified 2.5 years ago • written 2.5 years ago by bryantl • 90

Hi Bryantl, The galaxy was down yesterday, but i checked this morning and it was a miracle!!! Thanks so much! Have a nice day!

ADD REPLY • link written 2.5 years ago by kuick77 • 10
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