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Question: Cannot filer pileup result
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gravatar for wangshu12
2.8 years ago by
wangshu12 • 0
wangshu12 • 0 wrote:

I did MPileup, and I want to filer the pileup result to find the information I needed. However, the software says " no pileup dataset available". After MPileup, the dataset format is VCF. It should be recognized by the  "Filter pileup" tool.

Please help me to solve this problem.

Thanks

Shu
samtools • 719 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by wangshu12 • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

That particular tool uses pileup as a datatype input, not VCF. 

To obtain a pileup dataset, use the Mpileup or Generate pileup without the option genotype liklihood calculation. At the end of the run, the output will be in tabular format. Use the pencil icon to change the type to pileup and use the data with downstream tools, such as Filter Pileup.

To work with VCF datasets, see the tool group NGS: VCF Manipulation.

Details about all of these options are on the tool forms, both in the top option setting area and below in the help.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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