Varscan and pileup files

Question: Varscan and pileup files

2.8 years ago by

Hi,

I would like to perform a variant calling analysis using Varscan and I used Generate pileup under NGS: SAMtools directory , it completed the run generating a tabular format, but then Varscan in the " Pileup dataset" report "No pileup dataset available". How can I proceed?

galaxy • 1.1k views

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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by giulia.pregno • 0

2.8 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hi,

Did you check the datatype of your output in galaxy ? According to what you say the datatype should be "tabular", you need to set it to "pileup" so he can be available for varscan.

Cheers,

Christ

ADD COMMENT • link written 2.8 years ago by christophe.habib • 340

Hi,

thanks for the suggestion, I looked at the tool again but there is no place where I can select the output format, I report the explanations:

What it does

Uses SAMTools' pileup command to produce a pileup dataset from a provided BAM dataset. It generates two types of pileup datasets depending on the specified options. If Call consensus according to MAQ model? option is set to No, the tool produces simple pileup. If the option is set to Yes, a ten column pileup dataset with consensus is generated.

So I supposed there could be just the pileup as output result..

ADD REPLY • link written 2.8 years ago by giulia.pregno • 0

I used the same tool on my own instance and the format of the output is tabular.

If there is no option in the tool itself, you can still modify the datatype of your output itself after being created by using "edit attributes" (the little pen).

However you have to check that the output actually looks like a pileup before doing this.

ADD REPLY • link written 2.8 years ago by christophe.habib • 340

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The Pileup/Mpileup tools create pileup output with the datatype "tabular" assigned by default. These tabular datasets can have the datatype modified to be "pileup" for use with downstream tools.

Our team is updating the tools to create the output with the pileup datatype directly assigned, but it is currently not an option on the tool form.

Track progress on the change here, under the section "Issue by user interface behavior", item two:

https://github.com/jennaj/support-known-issues/wiki

Thanks, Jen, Galaxy team

ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

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